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Re: [tdwg-content] New Term Request - typifiedName
by Richard Pyle 04 Dec '13

04 Dec '13

Yes, I understand that as I mentioned. But what about my question regarding the same specimen being used to typify multiple taxa? Rich From: Gregor Hagedorn [mailto:gregor.hagedorn@mfn-berlin.de] Sent: Wednesday, December 04, 2013 7:16 PM To: Richard Pyle Cc: John R. Wieczorek; TDWG Content Mailing List Subject: Re: [tdwg-content] New Term Request - typifiedName I endorse Markus proposal enthusiastically. What Rich writes is appropriate if you use DwC in a structured way, with Identification instances that support a 1:n relation between specimen and identification instances. However, this cannot be assumed for all uses of DwC. Gregor On 4 December 2013 11:51, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hmmm..... This is the reason that typeStatus was included in the Identification class -- so that it always is associated with both a specimen (manifest as an occurrence), and to a taxon (name) -- to which the specimen is Identified. This is in keeping with what the concept of a "type specimen" really is -- that is, a specimen is not a type inherently, but rather a specimen is *designated* as a type by someone at some time, via an Identification instance. Of course, because DwC classes are not really intended to be used in an ontological sense, and because most Museums put their "typeStatus" field in their specimen table (rather than in an Identification table), I can certainly understand the need for this proposed new term. I guess my main concern/question is: how to deal with specimens that represent types of more than one name? (not common, but not necessarily an Edge-case either) Aloha, Rich > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content- > bounces(a)lists.tdwg.org] On Behalf Of John Wieczorek > Sent: Wednesday, December 04, 2013 4:13 AM > To: TDWG Content Mailing List > Subject: [tdwg-content] New Term Request - typifiedName > > Dear all, > > This message is to open public commentary on a request for a new term, > typifiedName, submitted by Markus Döring to the Darwin Core issue tracker > at https://code.google.com/p/darwincore/issues/detail?id=197. > The justification given for inclusion of the term is: > > "Clear separation of the type status and the typified scientific name that is > typified by a type specimen, the subject. Looking at how dwc:typeStatus has > been used in all of GBIFs specimen data one can see there is the need to > express this, but it should better be handled with a term on its own and > leave typeStatus for the status of the type only. The term name itself is also > used by ABCD: > http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcept0603." > > The proposal is as follows: > > Definition: > The scientific name that is based on the type specimen. > > Comment: > It is recommended to also indicate the typeStatus of the specimen. > > Refines: > > Has Domain: > > Has Range: > > Replaces: > > ABCD 2.06: > DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignation > s/NomenclaturalTypeDesignation/TypifiedName > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content -- -- --------------------------------- Dr. Gregor Hagedorn Head of Digital World Museum für Naturkunde Leibniz-Institut für Evolutions- und Biodiversitätsforschung Invalidenstrasse 43, 10115 Berlin +49 (0)30 2093 8576 <tel:%2B49%20%280%2930%202093%208576> (work) +49-(0)30-831 5785 <tel:%2B49-%280%2930-831%205785> (private) gregor.hagedorn(a)mfn-berlin.de http://www.naturkundemuseum-berlin.de http://linkedin.com/in/gregorhagedorn This communication, together with any attachments, is intended only for the person(s) to whom it is addressed. Redistributing or publishing it without permission may be a violation of copyright or privacy rights.

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Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent
by Éamonn Ó Tuama [GBIF] 26 Oct '13

26 Oct '13

Following all the excellent contributions on this list relating to expressing abundance data in Darwin Core, I think we may have uncovered a way that does not require any changes to the DwC standard. As has been pointed out, modelling sampling and abundance can be quite complex and challenging and is best done as an ontology (as in the work of the BCO). >From the GBIF perspective, our goal is to make it as simple as possible for data providers to deliver abundance data (in Darwin Core Archive format) that can support the science for processes such as CBD and IPBES. Here, I am using the term abundance (specifically population abundance) in the sense defined by GEO BON: "Quantity of individuals or biomass of a given taxon or functional group at a given location" [1]. The challenge is to come up with a way for Simple Darwin Core to express abundance data. It looks like we can probably work within the restrictions imposed by Simple Darwin Core [2] and use properties from MeasurementOrFact because, for the use case in question here, we only need to share one MeasurementOrFact per record. The model: A sample, associated with a sampling protocol has one or more taxon occurrence records each of which has an abundance measure which is expressed using MeasurementOrFact. At a minimum, we would need the following three MeasurementOrFact properties listed below (with definition and examples): measurementType The nature of the measurement, fact, characteristic, or assertion. Examples: "tail length", "temperature", "trap line length", "survey area", "trap type". For abundances we would use: count, percentage measurementValue The value of the measurement, fact, characteristic, or assertion. Examples: "45", "20", "1", "14.5", "UV-light". For abundances we would use any numeric value. measurementMethod A description of or reference to (publication, URI) the method or protocol used to determine the measurement, fact, characteristic, or assertion. Examples: "minimum convex polygon around burrow entrances" for a home range area, "barometric altimeter" for an elevation. For abundances we would use: Count/sq metre, count/litre, % of biovolume, % of species, ... To enable automated processing, we would need to develop a controlled list for measurementMethod and, ideally, there would also be a URI for the sampling protocol used which would be recorded in the dwc:samplingProtocol field. [1] http://www.earthobservations.org/documents/meetings/201202_geobon_ebv/30_ebv _species_table_v2.pdf [2] http://rs.tdwg.org/dwc/terms/simple/index.htm#rules -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of tdwg-content-request(a)lists.tdwg.org Sent: 26 September 2013 17:23 To: tdwg-content(a)lists.tdwg.org Subject: tdwg-content Digest, Vol 53, Issue 2 Send tdwg-content mailing list submissions to tdwg-content(a)lists.tdwg.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.tdwg.org/mailman/listinfo/tdwg-content or, via email, send a message with subject or body 'help' to tdwg-content-request(a)lists.tdwg.org You can reach the person managing the list at tdwg-content-owner(a)lists.tdwg.org When replying, please edit your Subject line so it is more specific than "Re: Contents of tdwg-content digest..." Today's Topics: 1. Re: Proposed new Darwin Core environmental terms from ENVO (John Wieczorek) 2. Re: Proposed new Darwin Core environmental terms from ENVO (John Wieczorek) 3. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 4. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Donald Hobern [GBIF]) 5. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Robert Guralnick) 6. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Chuck Miller) 7. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Donald Hobern [GBIF]) 8. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 9. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (John Wieczorek) 10. Re: Proposed new Darwin Core terms - abundance, abundanceAsPercent (Robert Guralnick) ---------------------------------------------------------------------- Message: 1 Date: Thu, 26 Sep 2013 14:44:34 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdOf7rMwQ3UCGGw1T53c4J7X=amJ_ibSkSX_WSb5EoqcA(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Dear all, The spirit of the proposal is to satisfy use cases defined in the document "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" found at http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO ontology. Steve is correct. All of the ENVO terms are classes in keeping with the OBO Foundry way of doing things. As such, they don't work in the intended Darwin Core context as they currently stand, where what we want are properties whose values can come from ENVO as a controlled vocabulary in the way Hilmar described. To satisfy the spirit of the proposal, I suggest that instead of replacing the dwc:habitat property with the envo:habitat class and adding the other three ENVO classes, we modify the existing dwc:habitat property and introduce new properties whose ranges are recommended to be the appropriate ENVO classes, as follows: Retain the property term dwc:habitat, but amend the definition to be: Term Name: habitat Identifier: http://rs.tdwg.org/dwc/terms/habitat Namespace: http://rs.tdwg.org/dwc/terms/ Label: Habitat Definition: A spatial region having environmental qualities which may sustain an organism or a community of organisms. Recommended best practice is to use a controlled vocabulary such as defined by the habitat class of the Environment Ontology (ENVO). Comment: Examples: "freshwater habitat", "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2008-11-19 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: habitat-2013-09-26 Replaces: habitat-2009-04-24 IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Add the following new property terms for biome, environmental feature, and environmental material: Term Name: biome Identifier: http://rs.tdwg.org/dwc/terms/biome Namespace: http://rs.tdwg.org/dwc/terms/ Label: Biome Definition: A major class of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and other factors like climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Biomes are often identified with particular patterns of ecological succession and climax vegetation. Recommended best practice is to use a controlled vocabulary such as defined by the biome class of the Environment Ontology (ENVO). Comment: Examples: "flooded grassland biome", "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: biome-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: environmentalFeature Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Feature Definition: A prominent or distinctive aspect, quality, or characteristic of a biome. Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Comment: Examples: "meadow", "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: environmentalFeature-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) Term Name: environmentalMaterial Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial Namespace: http://rs.tdwg.org/dwc/terms/ Label: Environmental Material Definition: Material in or on which organisms may live. Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO). Comment: Examples: "scum", "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see http://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified) Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: proposed Date Issued: 2013-09-26 Date Modified: 2013-09-26 Has Domain: Has Range: Refines: Version: environmentalMaterial-2013-09-26 Replaces: IsReplaceBy: Class: http://rs.tdwg.org/dwc/terms/Event ABCD 2.0.6: not in ABCD (someone please confirm or deny this) I hope this makes better sense. Cheers, John On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: > Well, the proposal says "The Darwin Core term habitat would be redefined..." > . I take that to mean that the term dwc:habitat is being replaced with > envo:00002036 . If that's not what it means, then it would be good to > clarify. If the intention is to provide values for other terms, that should > be stated. > > Steve > > > Hilmar Lapp wrote: > > I was assuming that the proposal was that subclasses of envo:habitat would > take the place of values for the dwc:habitat property. But perhaps I was > naive or misunderstanding? > > -hilmar > > Sent from away > > On Sep 25, 2013, at 8:23 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> > wrote: > > OK, now that I've had a chance to look at the RDF, it is as I suspected. If > I am understanding the proposal correctly, the proposal is to replace the > term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with the term > <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call > envo:00002036 for brevity) However, the definition of dwc:habitat which you > can view at > http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf > says > > dwc:habitat rdf:type rdfs:Property > > whereas the document I received at the end of those four redirects tells me > that > > envo:00002036 rdf:type owl:Class > > Since > > owl:Class rdfs:subclassOf rdfs:Class > > then we are effectively changing the current DwC "habitat" term from a > property into a class similar to dwc:Occurrence, dwc:Identification, > dwc:Taxon, etc. which are all of type rdfs:Class. > > So I'm left wondering what I can do with the new term. With the old term I > could make a statement like > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat "deciduous > forest" > > or something like that if I take the hint from the DwC class groupings that > dwc:habitat might be a property of dwc:Event instances. But I can't > meaningfully say > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036 > "deciduous forest" > > That doesn't make any sense because the way I understand RDF, predicates > should be properties, not classes. Even if we weren't talking about RDF, > I'd still have the same problem (we are changing a property into a class) - > it's just easier for me to make plain what the issue is by giving RDF > examples. So just exactly what can I "do" with envo:00002036 ????? > > I haven't looked up the RDF for the other proposed terms (too much work with > the four redirects), but I suspect if I did, I'd find that they are also > classes and not properties. This particular issue is a case of a broader > issue that I have about OBO-style ontologies. They are great for defining > how many, many kinds of classes are related to each other. But they provide > very few properties that could be used as predicates to serve as properties > of instance data. > > Steve > > John Wieczorek wrote: > > Dear all, > > GBIF has just published "Meeting Report: GBIF hackathon-workshop on > Darwin Core and sample data (22-24 May 2013)" at > http://www.gbif.org/orc/?doc_id=5424. Now that this document is > available for public reference, I would like to formally open the > minimum 30-day comment period on the new environmental terms proposed > during the workshop and defined in the referenced document. > > The formal proposal would change the term habitat to align it with the > ENVO habitat term. The related issues in the Darwin Core issue tracker > is https://code.google.com/p/darwincore/issues/detail?id=178. The > Darwin Core term habitat would be redefined as follows: > > Term Name: habitat > Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 > Namespace: http://purl.obolibrary.org/obo/ > Label: Habitat > Definition: A spatial region having environmental qualities which may > sustain an organism or a community of organisms. > Comment: Examples: "freshwater habitat", > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2008-11-19 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00002036 > Replaces: habitat-2009-04-24 > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > The formal proposal would add the following new terms for biome, > environmental feature, and environmental material: > > Term Name: biome > Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 > Namespace: http://purl.obolibrary.org/obo/ > Label: Biome > Definition: A major class of ecologically similar communities of > plants, animals, and other organisms. Biomes are defined based on > factors such as plant structures (such as trees, shrubs, and grasses), > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > woodland, savanna), and other factors like climate. Unlike ecozones, > biomes are not defined by genetic, taxonomic, or historical > similarities. Biomes are often identified with particular patterns of > ecological succession and climax vegetation. > Comment: Examples: "flooded grassland biome", > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00000428 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmental feature > Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 > Namespace: http://purl.obolibrary.org/obo/ > Label: Environmental Feature > Definition: A prominent or distinctive aspect, quality, or > characteristic of a biome. > Comment: Examples: "meadow", > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00002297 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmental material > Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 > Namespace: http://purl.obolibrary.org/obo/ > Label: Environmental Material > Definition: Material in or on which organisms may live. > Comment: Examples: "scum", > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > Refines: > Status: proposed > Date Issued: 2013-09-25 > Date Modified: 2013-09-25 > Has Domain: > Has Range: > Refines: > Version: http://purl.obolibrary.org/obo/ENVO_00010483 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > The related issues in the Darwin Core issue tracker are > https://code.google.com/p/darwincore/issues/detail?id=189 > https://code.google.com/p/darwincore/issues/detail?id=190 > and > https://code.google.com/p/darwincore/issues/detail?id=191 > > If there are any objections to the changes proposed for these terms, > or comments about their definitions, please respond to this message. > If there are no objections or if consensus can be reached on any > amendments put forward, the proposal will go before the Executive > Committee for authorization to put these additions into effect after > the public commentary period. > > Cheers, > > John > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > . > > > > > -- > 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 > > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > -- > 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 ------------------------------ Message: 2 Date: Thu, 26 Sep 2013 14:51:13 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO To: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdARDj32v9EPaofwHrzwonQ3czgwMaiyDmnj3c7L0tMnA(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 I've been in communication with the OBO-ENVO group (obo-envo(a)lists.sourceforge.net) about the proposed re-use of the ENVO terms. The ENVO ontology remains in active development, with a proposed forthcoming guide on how to use ENVO. I have agreed to forward an invitation extended by Pier Buttigieg to the TDWG community to actively contribute. "To be clear, the habitat class itself isn't queued for obsoletion, but its current subclasses are. Once habitat is better-defined, new subclasses will be created. If anyone in TDWG wishes to help shape the definition of this concept or share any observations to promote its usefulness to the biodiversity community we're certainly open to input." On Thu, Sep 26, 2013 at 2:44 PM, John Wieczorek <tuco(a)berkeley.edu> wrote: > Dear all, > > The spirit of the proposal is to satisfy use cases defined in the > document "Meeting Report: GBIF hackathon-workshop on > Darwin Core and sample data (22-24 May 2013)" found at > http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO > ontology. Steve is correct. All of the ENVO terms are classes in > keeping with the OBO Foundry way of doing things. As such, they don't > work in the intended Darwin Core context as they currently stand, > where what we want are properties whose values can come from ENVO as a > controlled vocabulary in the way Hilmar described. > > To satisfy the spirit of the proposal, I suggest that instead of > replacing the dwc:habitat property with the envo:habitat class and > adding the other three ENVO classes, we modify the existing > dwc:habitat property and introduce new properties whose ranges are > recommended to be the appropriate ENVO classes, as follows: > > Retain the property term dwc:habitat, but amend the definition to be: > > Term Name: habitat > Identifier: http://rs.tdwg.org/dwc/terms/habitat > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Habitat > Definition: A spatial region having environmental qualities which may > sustain an organism or a community of organisms. Recommended best > practice is to use a controlled vocabulary such as defined by the > habitat class of the Environment Ontology (ENVO). > Comment: Examples: "freshwater habitat", > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2008-11-19 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: habitat-2013-09-26 > Replaces: habitat-2009-04-24 > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Add the following new property terms for biome, > environmental feature, and environmental material: > > Term Name: biome > Identifier: http://rs.tdwg.org/dwc/terms/biome > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Biome > Definition: A major class of ecologically similar communities of > plants, animals, and other organisms. Biomes are defined based on > factors such as plant structures (such as trees, shrubs, and grasses), > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > woodland, savanna), and other factors like climate. Unlike ecozones, > biomes are not defined by genetic, taxonomic, or historical > similarities. Biomes are often identified with particular patterns of > ecological succession and climax vegetation. Recommended best practice > is to use a controlled vocabulary such as defined by the biome class > of the Environment Ontology (ENVO). > Comment: Examples: "flooded grassland biome", > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: biome-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmentalFeature > Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Environmental Feature > Definition: A prominent or distinctive aspect, quality, or > characteristic of a biome. Recommended best practice is to use a > controlled vocabulary such as defined by the environmental feature > class of the Environment Ontology (ENVO). > Comment: Examples: "meadow", > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: environmentalFeature-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > Term Name: environmentalMaterial > Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial > Namespace: http://rs.tdwg.org/dwc/terms/ > Label: Environmental Material > Definition: Material in or on which organisms may live. Recommended > best practice is to use a controlled vocabulary such as defined by the > environmental feature class of the Environment Ontology (ENVO). > Comment: Examples: "scum", > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > http://code.google.com/p/darwincore/wiki/Event (there will be no > further documentation here until the term is ratified) > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > Refines: > Status: proposed > Date Issued: 2013-09-26 > Date Modified: 2013-09-26 > Has Domain: > Has Range: > Refines: > Version: environmentalMaterial-2013-09-26 > Replaces: > IsReplaceBy: > Class: http://rs.tdwg.org/dwc/terms/Event > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > I hope this makes better sense. > > Cheers, > > John > > On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf > <steve.baskauf(a)vanderbilt.edu> wrote: >> Well, the proposal says "The Darwin Core term habitat would be redefined..." >> . I take that to mean that the term dwc:habitat is being replaced with >> envo:00002036 . If that's not what it means, then it would be good to >> clarify. If the intention is to provide values for other terms, that should >> be stated. >> >> Steve >> >> >> Hilmar Lapp wrote: >> >> I was assuming that the proposal was that subclasses of envo:habitat would >> take the place of values for the dwc:habitat property. But perhaps I was >> naive or misunderstanding? >> >> -hilmar >> >> Sent from away >> >> On Sep 25, 2013, at 8:23 PM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> >> wrote: >> >> OK, now that I've had a chance to look at the RDF, it is as I suspected. If >> I am understanding the proposal correctly, the proposal is to replace the >> term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with the term >> <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call >> envo:00002036 for brevity) However, the definition of dwc:habitat which you >> can view at >> http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf >> says >> >> dwc:habitat rdf:type rdfs:Property >> >> whereas the document I received at the end of those four redirects tells me >> that >> >> envo:00002036 rdf:type owl:Class >> >> Since >> >> owl:Class rdfs:subclassOf rdfs:Class >> >> then we are effectively changing the current DwC "habitat" term from a >> property into a class similar to dwc:Occurrence, dwc:Identification, >> dwc:Taxon, etc. which are all of type rdfs:Class. >> >> So I'm left wondering what I can do with the new term. With the old term I >> could make a statement like >> >> <http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat "deciduous >> forest" >> >> or something like that if I take the hint from the DwC class groupings that >> dwc:habitat might be a property of dwc:Event instances. But I can't >> meaningfully say >> >> <http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036 >> "deciduous forest" >> >> That doesn't make any sense because the way I understand RDF, predicates >> should be properties, not classes. Even if we weren't talking about RDF, >> I'd still have the same problem (we are changing a property into a class) - >> it's just easier for me to make plain what the issue is by giving RDF >> examples. So just exactly what can I "do" with envo:00002036 ????? >> >> I haven't looked up the RDF for the other proposed terms (too much work with >> the four redirects), but I suspect if I did, I'd find that they are also >> classes and not properties. This particular issue is a case of a broader >> issue that I have about OBO-style ontologies. They are great for defining >> how many, many kinds of classes are related to each other. But they provide >> very few properties that could be used as predicates to serve as properties >> of instance data. >> >> Steve >> >> John Wieczorek wrote: >> >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on the new environmental terms proposed >> during the workshop and defined in the referenced document. >> >> The formal proposal would change the term habitat to align it with the >> ENVO habitat term. The related issues in the Darwin Core issue tracker >> is https://code.google.com/p/darwincore/issues/detail?id=178. The >> Darwin Core term habitat would be redefined as follows: >> >> Term Name: habitat >> Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Habitat >> Definition: A spatial region having environmental qualities which may >> sustain an organism or a community of organisms. >> Comment: Examples: "freshwater habitat", >> "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2008-11-19 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00002036 >> Replaces: habitat-2009-04-24 >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The formal proposal would add the following new terms for biome, >> environmental feature, and environmental material: >> >> Term Name: biome >> Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Biome >> Definition: A major class of ecologically similar communities of >> plants, animals, and other organisms. Biomes are defined based on >> factors such as plant structures (such as trees, shrubs, and grasses), >> leaf types (such as broadleaf and needleleaf), plant spacing (forest, >> woodland, savanna), and other factors like climate. Unlike ecozones, >> biomes are not defined by genetic, taxonomic, or historical >> similarities. Biomes are often identified with particular patterns of >> ecological succession and climax vegetation. >> Comment: Examples: "flooded grassland biome", >> "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00000428 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: environmental feature >> Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Environmental Feature >> Definition: A prominent or distinctive aspect, quality, or >> characteristic of a biome. >> Comment: Examples: "meadow", >> "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00002297 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: environmental material >> Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 >> Namespace: http://purl.obolibrary.org/obo/ >> Label: Environmental Material >> Definition: Material in or on which organisms may live. >> Comment: Examples: "scum", >> "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see >> http://code.google.com/p/darwincore/wiki/Event (there will be no >> further documentation here until the term is ratified) >> Type of Term: http://www.w3.org/2000/01/rdf-schema#Class >> Refines: >> Status: proposed >> Date Issued: 2013-09-25 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: http://purl.obolibrary.org/obo/ENVO_00010483 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Event >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=189 >> https://code.google.com/p/darwincore/issues/detail?id=190 >> and >> https://code.google.com/p/darwincore/issues/detail?id=191 >> >> If there are any objections to the changes proposed for these terms, >> or comments about their definitions, please respond to this message. >> If there are no objections or if consensus can be reached on any >> amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> . >> >> >> >> >> -- >> 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 >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> >> -- >> 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 ------------------------------ Message: 3 Date: Thu, 26 Sep 2013 15:48:16 +0200 From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CAHwKGGdrmyEAwZ-TcTxUqcdGemwc330_H51XUTo9abb0Mez8-g(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Could every concept of abundance be captured in a combination of abundance, abundanceUnit, abundanceMethod? If so, is there justification for creating new terms at all if the concepts can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the following properties? measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> wrote: > Thanks - I think I too have missed something. If we want to make these > terms usable, there needs to be a simple way to get numbers out of records > that can be compared with one another where sampling methods allow such > comparisons. The suggested plain text examples for Abundance don't make > this possible. Forcing normalisation into percentages seems an unnecessary > hurdle and risks encouraging the impression that number of ducks on a > reservoir is somehow comparable with percentage dry mass, proportional > expression of CO1 for a particular species in an ecogenomics sample, or > whatever. > > I would much rather we ensured we had a standard, preferred field which the > data publisher can populate directly with whatever number is the most > appropriate expression of the relative abundance in the sample. That gives > consumers a clear expectation of how to interpret and handle it. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org > Global Biodiversity Information Facility http://www.gbif.org/ > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De Wever > Sent: Thursday, September 26, 2013 8:44 AM > To: tuco(a)berkeley.edu; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, > abundanceAsPercent > > Dear all, > > As somewhat of an outsider I have another question with regards to the > proposed terms abundance and abundanceAsPercent. > > Is there a specific reason for not adopting: > * the abundance field as a field to store only the value and > * a field abundanceUnit/abundanceType to specify whether the value is in % > of species, % of biovolume, % of biomass, individuals/l, ind./m^2, ind/m^3, > ind./sampling effort,...(instead of having a field specific for %)? > > Maybe this has been discussed during the hackathon and I missed it in the > report? > > Thanks for considering this question. > > With best regards, > Aaike > > John Wieczorek wrote: >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on two related new terms proposed during >> the workshop and defined in the referenced document. >> >> The formal proposal would add the following new terms: >> >> Term Name: abundance >> Identifier: http://rs.tdwg.org/dwc/terms/abundance >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance >> Definition: The number of individuals of a taxon found in a sample. >> This is typically expressed as number per unit of area or volume. In >> the case of vegetation and colonial/encrusting species, percent cover >> can be used. >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", >> "24%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-03-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundance-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: abundanceAsPercent >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance as Percent >> Definition: 100 times the number of individuals of a taxon found in a >> sample divided by the total number of individuals of all taxa in the >> sample. >> Comment: Examples: "2.4%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-08-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundanceAsPercent-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=142 >> and >> https://code.google.com/p/darwincore/issues/detail?id=187 >> >> If there are any objections to the changes proposed for these new >> terms, or comments about their definitions, please respond to this >> message. If there are no objections or if consensus can be reached on >> any amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- > Aaike De Wever > BioFresh Science Officer > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > Vautierstraat 29, 1000 Brussels Belgium > tel.: +32(0)2 627 43 90 > mobile.: +32(0)486 28 05 93 > email: <aaike.dewever(a)naturalsciences.be> > skype: aaikew > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > <http://data.freshwaterbiodiversity.eu/> > Belgian Biodiversity Platform: <http://www.biodiversity.be> > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > ------------------------------ Message: 4 Date: Thu, 26 Sep 2013 16:01:10 +0200 From: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: <tuco(a)berkeley.edu> Cc: 'TDWG Content Mailing List' <tdwg-content(a)lists.tdwg.org> Message-ID: <01fd01cebac0$da9a8550$8fcf8ff0$(a)gbif.org> Content-Type: text/plain; charset="iso-8859-1" Thanks, John. You are correct. I think though that abundance is such a commonly needed property that it would be a mistake not to make it work easily even in Simple Darwin Core. Donald ---------------------------------------------------------------------- Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity Information Facility http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 ---------------------------------------------------------------------- -----Original Message----- From: gtuco.btuco(a)gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of John Wieczorek Sent: Thursday, September 26, 2013 3:48 PM To: Donald Hobern [GBIF] Cc: aaike.dewever(a)naturalsciences.be; TDWG Content Mailing List Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent Could every concept of abundance be captured in a combination of abundance, abundanceUnit, abundanceMethod? If so, is there justification for creating new terms at all if the concepts can be captured in MeasurentsOrFacts (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the following properties? measurementType measurementValue measurementAccuracy measurementUnit measurementDeterminedDate measurementDeterminedBy measurementMethod measurementRemarks The only drawback I can see is that with MeasurementOrFacts you could not share the abunance information in Simple Darwin Core. To understand why, see http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> wrote: > Thanks - I think I too have missed something. If we want to make > these terms usable, there needs to be a simple way to get numbers out > of records that can be compared with one another where sampling > methods allow such comparisons. The suggested plain text examples for > Abundance don't make this possible. Forcing normalisation into > percentages seems an unnecessary hurdle and risks encouraging the > impression that number of ducks on a reservoir is somehow comparable > with percentage dry mass, proportional expression of CO1 for a > particular species in an ecogenomics sample, or whatever. > > I would much rather we ensured we had a standard, preferred field > which the data publisher can populate directly with whatever number is > the most appropriate expression of the relative abundance in the > sample. That gives consumers a clear expectation of how to interpret and handle it. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity > Information Facility http://www.gbif.org/ GBIF Secretariat, > Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De > Wever > Sent: Thursday, September 26, 2013 8:44 AM > To: tuco(a)berkeley.edu; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - > abundance, abundanceAsPercent > > Dear all, > > As somewhat of an outsider I have another question with regards to the > proposed terms abundance and abundanceAsPercent. > > Is there a specific reason for not adopting: > * the abundance field as a field to store only the value and > * a field abundanceUnit/abundanceType to specify whether the value is > in % of species, % of biovolume, % of biomass, individuals/l, > ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field specific for %)? > > Maybe this has been discussed during the hackathon and I missed it in > the report? > > Thanks for considering this question. > > With best regards, > Aaike > > John Wieczorek wrote: >> Dear all, >> >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on >> Darwin Core and sample data (22-24 May 2013)" at >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is >> available for public reference, I would like to formally open the >> minimum 30-day comment period on two related new terms proposed >> during the workshop and defined in the referenced document. >> >> The formal proposal would add the following new terms: >> >> Term Name: abundance >> Identifier: http://rs.tdwg.org/dwc/terms/abundance >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance >> Definition: The number of individuals of a taxon found in a sample. >> This is typically expressed as number per unit of area or volume. In >> the case of vegetation and colonial/encrusting species, percent cover >> can be used. >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", >> "24%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-03-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundance-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> Term Name: abundanceAsPercent >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent >> Namespace: http:/rs.tdwg.org/dwc/terms/ >> Label: Abundance as Percent >> Definition: 100 times the number of individuals of a taxon found in a >> sample divided by the total number of individuals of all taxa in the >> sample. >> Comment: Examples: "2.4%". For discussion see >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no >> further documentation here until the term is ratified) Type of Term: >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property >> Refines: >> Status: proposed >> Date Issued: 2012-08-01 >> Date Modified: 2013-09-25 >> Has Domain: >> Has Range: >> Refines: >> Version: abundanceAsPercent-2013-09-25 >> Replaces: >> IsReplaceBy: >> Class: http://rs.tdwg.org/dwc/terms/Occurrence >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) >> >> The related issues in the Darwin Core issue tracker are >> https://code.google.com/p/darwincore/issues/detail?id=142 >> and >> https://code.google.com/p/darwincore/issues/detail?id=187 >> >> If there are any objections to the changes proposed for these new >> terms, or comments about their definitions, please respond to this >> message. If there are no objections or if consensus can be reached on >> any amendments put forward, the proposal will go before the Executive >> Committee for authorization to put these additions into effect after >> the public commentary period. >> >> Cheers, >> >> John >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- > Aaike De Wever > BioFresh Science Officer > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > Vautierstraat 29, 1000 Brussels Belgium > tel.: +32(0)2 627 43 90 > mobile.: +32(0)486 28 05 93 > email: <aaike.dewever(a)naturalsciences.be> > skype: aaikew > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > <http://data.freshwaterbiodiversity.eu/> > Belgian Biodiversity Platform: <http://www.biodiversity.be> > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > ------------------------------ Message: 5 Date: Thu, 26 Sep 2013 08:37:15 -0600 From: Robert Guralnick <Robert.Guralnick(a)colorado.edu> Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, abundanceAsPercent To: "Donald Hobern [GBIF]" <dhobern(a)gbif.org> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <CADAgxGX=ZRknz2T-kd0e9wwwP72pSrtoeRVb175fm1EQQ7iovQ(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" I agree with Donald here regarding the need for Abundance, but am, to be honest, not quite I understand (or agree) with the logic of the proposal. Abundance is listed as a property of an occurrence, and I wonder if that make sense given the class definition "The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.)" Is abundance "evidence of an occurrence in nature". To me, abundance is a property of a survey and its associated methodology and is based on multiple occurrences that come from a sample and a definition of extent. It seems to me to be a bad fit to scrunch abundance into the occurrence class. I recognize that it might not quite fit anywhere in DwC yet. Wouldn't it be better to wait to see if materialSample is ratified as a class within the Darwin Core? Best, Rob On Thu, Sep 26, 2013 at 8:01 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org>wrote: > Thanks, John. > > You are correct. I think though that abundance is such a commonly needed > property that it would be a mistake not to make it work easily even in > Simple Darwin Core. > > Donald > > ---------------------------------------------------------------------- > Donald Hobern - GBIF Director - dhobern(a)gbif.org > Global Biodiversity Information Facility http://www.gbif.org/ > GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > ---------------------------------------------------------------------- > > > -----Original Message----- > From: gtuco.btuco(a)gmail.com [mailto:gtuco.btuco@gmail.com] On Behalf Of > John > Wieczorek > Sent: Thursday, September 26, 2013 3:48 PM > To: Donald Hobern [GBIF] > Cc: aaike.dewever(a)naturalsciences.be; TDWG Content Mailing List > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - abundance, > abundanceAsPercent > > Could every concept of abundance be captured in a combination of abundance, > abundanceUnit, abundanceMethod? > > If so, is there justification for creating new terms at all if the concepts > can be captured in MeasurentsOrFacts > (http://rs.tdwg.org/dwc/terms/index.htm#measureindex) which have the > following properties? > > measurementType > measurementValue > measurementAccuracy > measurementUnit > measurementDeterminedDate > measurementDeterminedBy > measurementMethod > measurementRemarks > > The only drawback I can see is that with MeasurementOrFacts you could not > share the abunance information in Simple Darwin Core. To understand why, > see > http://rs.tdwg.org/dwc/terms/simple/index.htm#rules. > > > On Thu, Sep 26, 2013 at 10:50 AM, Donald Hobern [GBIF] <dhobern(a)gbif.org> > wrote: > > Thanks - I think I too have missed something. If we want to make > > these terms usable, there needs to be a simple way to get numbers out > > of records that can be compared with one another where sampling > > methods allow such comparisons. The suggested plain text examples for > > Abundance don't make this possible. Forcing normalisation into > > percentages seems an unnecessary hurdle and risks encouraging the > > impression that number of ducks on a reservoir is somehow comparable > > with percentage dry mass, proportional expression of CO1 for a > > particular species in an ecogenomics sample, or whatever. > > > > I would much rather we ensured we had a standard, preferred field > > which the data publisher can populate directly with whatever number is > > the most appropriate expression of the relative abundance in the > > sample. That gives consumers a clear expectation of how to interpret and > handle it. > > > > Donald > > > > ---------------------------------------------------------------------- > > Donald Hobern - GBIF Director - dhobern(a)gbif.org Global Biodiversity > > Information Facility http://www.gbif.org/ GBIF Secretariat, > > Universitetsparken 15, DK-2100 Copenhagen ?, Denmark > > Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 > > ---------------------------------------------------------------------- > > > > > > -----Original Message----- > > From: tdwg-content-bounces(a)lists.tdwg.org > > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Aaike De > > Wever > > Sent: Thursday, September 26, 2013 8:44 AM > > To: tuco(a)berkeley.edu; TDWG Content Mailing List > > Subject: Re: [tdwg-content] Proposed new Darwin Core terms - > > abundance, abundanceAsPercent > > > > Dear all, > > > > As somewhat of an outsider I have another question with regards to the > > proposed terms abundance and abundanceAsPercent. > > > > Is there a specific reason for not adopting: > > * the abundance field as a field to store only the value and > > * a field abundanceUnit/abundanceType to specify whether the value is > > in % of species, % of biovolume, % of biomass, individuals/l, > > ind./m^2, ind/m^3, ind./sampling effort,...(instead of having a field > specific for %)? > > > > Maybe this has been discussed during the hackathon and I missed it in > > the report? > > > > Thanks for considering this question. > > > > With best regards, > > Aaike > > > > John Wieczorek wrote: > >> Dear all, > >> > >> GBIF has just published "Meeting Report: GBIF hackathon-workshop on > >> Darwin Core and sample data (22-24 May 2013)" at > >> http://www.gbif.org/orc/?doc_id=5424. Now that this document is > >> available for public reference, I would like to formally open the > >> minimum 30-day comment period on two related new terms proposed > >> during the workshop and defined in the referenced document. > >> > >> The formal proposal would add the following new terms: > >> > >> Term Name: abundance > >> Identifier: http://rs.tdwg.org/dwc/terms/abundance > >> Namespace: http:/rs.tdwg.org/dwc/terms/ > >> Label: Abundance > >> Definition: The number of individuals of a taxon found in a sample. > >> This is typically expressed as number per unit of area or volume. In > >> the case of vegetation and colonial/encrusting species, percent cover > >> can be used. > >> Comment: Examples: "4 per square meter", "0.32 per cubic meter", > >> "24%". For discussion see > >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no > >> further documentation here until the term is ratified) Type of Term: > >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > >> Refines: > >> Status: proposed > >> Date Issued: 2012-03-01 > >> Date Modified: 2013-09-25 > >> Has Domain: > >> Has Range: > >> Refines: > >> Version: abundance-2013-09-25 > >> Replaces: > >> IsReplaceBy: > >> Class: http://rs.tdwg.org/dwc/terms/Occurrence > >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > >> > >> Term Name: abundanceAsPercent > >> Identifier: http://rs.tdwg.org/dwc/terms/abundanceAsPercent > >> Namespace: http:/rs.tdwg.org/dwc/terms/ > >> Label: Abundance as Percent > >> Definition: 100 times the number of individuals of a taxon found in a > >> sample divided by the total number of individuals of all taxa in the > >> sample. > >> Comment: Examples: "2.4%". For discussion see > >> http://code.google.com/p/darwincore/wiki/Occurrence (there will be no > >> further documentation here until the term is ratified) Type of Term: > >> http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > >> Refines: > >> Status: proposed > >> Date Issued: 2012-08-01 > >> Date Modified: 2013-09-25 > >> Has Domain: > >> Has Range: > >> Refines: > >> Version: abundanceAsPercent-2013-09-25 > >> Replaces: > >> IsReplaceBy: > >> Class: http://rs.tdwg.org/dwc/terms/Occurrence > >> ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > >> > >> The related issues in the Darwin Core issue tracker are > >> https://code.google.com/p/darwincore/issues/detail?id=142 > >> and > >> https://code.google.com/p/darwincore/issues/detail?id=187 > >> > >> If there are any objections to the changes proposed for these new > >> terms, or comments about their definitions, please respond to this > >> message. If there are no objections or if consensus can be reached on > >> any amendments put forward, the proposal will go before the Executive > >> Committee for authorization to put these additions into effect after > >> the public commentary period. > >> > >> Cheers, > >> > >> John > >> _______________________________________________ > >> tdwg-content mailing list > >> tdwg-content(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > -- > > Aaike De Wever > > BioFresh Science Officer > > Freshwater Laboratory, Royal Belgian Institute of Natural Sciences > > Vautierstraat 29, 1000 Brussels Belgium > > tel.: +32(0)2 627 43 90 > > mobile.: +32(0)486 28 05 93 > > email: <aaike.dewever(a)naturalsciences.be> > > skype: aaikew > > LinkedIn: <http://be.linkedin.com/in/aaikedewever> > > BioFresh: <http://www.freshwaterbiodiversity.eu/> and > > <http://data.freshwaterbiodiversity.eu/> > > Belgian Biodiversity Platform: <http://www.biodiversity.be> > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content >

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Workshop on Documenting Darwin Core
by joel sachs 25 Oct '13

25 Oct '13

Everyone, The Documenting Darwin Core workshop being held next week at TDWG will be a series of four facilitated discussions that will examine current usage and documentation of some of the more contentious and/or misunderstood Darwin Core terms. Descriptions and goals for each session are posted at http://bit.ly/18U2V2b . Please feel free to comment on this agenda. All are welcome to participate in any or all of the sessions. But please note that we will only have time for minimal introductory and background discussion. For those who need a refresher course, I've pasted links to issue summaries below. To all who'll be attending, I wish safe travels and a wonderful and productive meeting - I wish I could be there. Best, Joel. --- The trouble with Occurrence, in a nutshell: http://lists.tdwg.org/pipermail/tdwg-content/2013-June/003035.html The proposal to add the classes for Individuals and Evidence (currently labeled "Organism" and "CollectionObject", respectively): http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html How rdf:type relates to dwc:basisOfRecord: http://code.google.com/p/tdwg-rdf/wiki/DwcRdfGuideProposal (section 2.3.1.4) This month's thread on basisOfRecord: http://lists.tdwg.org/pipermail/tdwg-content/2013-October/003150.html And, for extra credit: http://code.google.com/p/tdwg-rdf/wiki/DarwinCoreClasses (particularly the section on Occurrence)

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Darwin Core Standard evolves to include Material Sample
by John Wieczorek 25 Oct '13

25 Oct '13

Dear all, The proposal for the addition of the MaterialSample terms to the Darwin Core was ratified by the TDWG Executive Committee on 9 Oct 2013. I have been implementing all of the changes necessary to the standard since then. I have just finished publishing the last of the updates to the Darwin Core web site [1] and the Darwin Core Project web site [2]. A log of all of the changes made over time can be seen in the change logs at [3]. Congratulations, community, on working together to let Darwin Core evolve to meet new and continuing needs. Cheers, John [1] http://rs.tdwg.org/dwc/ [2] https://code.google.com/p/darwincore/ [3] https://code.google.com/p/darwincore/source/list

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What can Global Biodiversity Information Facility (GBIF) do for you?
by Roderic Page 17 Oct '13

17 Oct '13

I sent a version of this message to TAXACOM and EvolDir, so you may have seen it already (in which case my apologies), but I've been appointed Chair of the GBIF Science Committee and I'm canvasing views on what's next for GBIF, particularly regarding the kinds of data it collects and the kinds of science it supports (you can get an idea of the kind of science that GBIF-hosted data currently supports from this list of papers on Mendeley http://www.mendeley.com/groups/1068301/gbif-public-library/ ). I should stress that this is simply me trying to calibrate my perception of GBIF's role with what others think. There have been formal surveys (see the papers in the journal "Biodiversity Informatics" https://journals.ku.edu/index.php/jbi/issue/view/370/showToc ), meetings, and a "vision" statement (the "Global Biodiversity Informatics Outlook, http://www.biodiversityinformatics.org/ ). But there's always the chance that these fora may miss some points of view, so I'm keen to get feedback on what sort of things GBIF could do to improve the way it can help people tackle the scientific questions they are interested in. For example, is there some fundamental limitation that GBIF has that prevents it being useful to you? Is there some feature/data type/geographic coverage/etc. that could be addressed that would make it more useful? Is there a role that GBIF should take on that it hasn't done so? I'd welcome any comments, suggestions, views, etc. You can reply to me directly, or to this email list. I've also posted this request on my blog http://iphylo.blogspot.co.uk/2013/10/what-can-global-biodiversity.html, so you can comment there if you like. Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.page(a)bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 Skype: rdmpage Facebook: http://www.facebook.com/rdmpage LinkedIn: http://uk.linkedin.com/in/rdmpage Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ ORCID: http://orcid.org/0000-0002-7101-9767

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Re: [tdwg-content] A plea around basisOfRecord
by Ramona Walls 16 Oct '13

16 Oct '13

There is a lot of content here, but let me try to address a few topics. >From Donald's original email: >> 2. basisOfRecord values should be taken from a hierarchical >> vocabulary with three main branches: >> a. ?specimens? (i.e. biological material that can be >> reviewed), with a hierarchy of subordinate values such as >> ?pinnedSpecimen?, ?herbariumSheet?, etc. >> b. derived, non-biological evidence (not sure what name), >> with a hierarchy of subordinate values such as ?dnaSequence?, >> ?soundRecording?, ?stillImage?, etc. >> c. asserted observations with no revisitable evidence other >> than the authority of the observer I agree with the idea of having basis of record organized as a hierarchical vocabulary (preferably as an ontology), but disagree with the proposed hierarchy, mostly because b groups fundamentally different types of entities. The BCO is working on just such a hierarchy, and could easily include any terms needed for basis of record. If the exact subclassOf hierarchy of the BCO is not ideal for Darwin Core, syntactic classes that group terms based on other criteria can be used for DwC. >> 3. TDWG should deliver a basic ontology in the form of a >> graph of key relationships between the most significant >> conceptual entities in our world (TaxonName, TaxonConcept, >> Identification, Collection, Specimen, Locality, Agent, ?) The BCO could serve as this basic ontology for TDWG. Some additional classes would be needed, and maybe those could come from the TDWG ontology (but I would need to look into that). The BCO is intended to serve a broader need than just linking Darwin Core archives, but it is a simple matter to make a subset that would serve the specific needs of TDWG. The advantage of using BCO is that it is designed to be compatible with other kinds of life science ontologies and data, which makes it more flexible and more likely that it will fulfill unforseen future needs. I (along with co-authors) plan to give some more background on this approach in a talk at TDWG in a few weeks. I am not ruling out DSW as a potential solution, either. My main concerns with DSW are 1) it is tightly coupled to the Darwin Core and therefor inherits some of the limitations of the Darwin Core. 2) many of the classes and relations are application specific, and therefor not interpretable outside the context of the application. I am looking forward to learning more about DSW at the upcoming TDWG meeting, where I expect there will be lengthy discussions of the relative merits of DSW versus BCO. Both ontologies will be presented in the same session. >> 4. This ontology should not attempt to map all the >> complexity of biodiversity-related data ? just provide the >> high-level map and key relationships (TaxonConcept hasName >> TaxonName, Specimen heldIn Collection, etc.) ? it should leave >> definition of other properties as a separate, open-ended activity >> for the community The BCO is more of an open-ended activity that attempts to model of biodiversity, but, as I mentioned above, subsets can be created for more specific needs. In contrast, creating small, application-specific ontologies for every application does little to overcome the problem of data silos. When everyone makes their own ontology, we are not any better off than when there are no ontologies. >> 5. This ontology should be reviewed at regular intervals >> and versioned as necessary to address critical gaps ? provided >> that backwards compatibility is maintained (splitting a class >> into multiple consitituent classes probably won?t break anything, >> so start simple) An essential part of any ontology is maintenance. >> 7. Every Darwin Core term should be documented to be >> tightly associated with a single, fixed class in the ontology >> (e.g. scientificName and specificEpithet are ALWAYS considered to >> be properties of a TaxonName whether or not that TaxonName object >> is clearly referenced or separated out) What I see as one of the fundamental problems with DwC is that the bulk of the terms are properties. That means that when data suppliers enter data in a spread sheet, they are entering literals or URIs that are the objects of these properties. Having hundreds of properties that are unique to DwC seriously limits the interoperability of DwC tagged data sets (as I mentioned in response to point 4). I think a better solution would be to create ontology classes for most of the DwC terms (along with a few properties), and then create data annotations that are instances of those classes. That is a much more common way of organizing ontology-annotated data and would allow reasoners to work over the data. However, this would be a fundamental change to the nature of the Darwin Core. >> 8. Every data publisher should be encouraged to share all >> relevant data elements in their source data in the most >> convenient normalised or denormalised form, provided they use the >> recognised Darwin Core properties for elements that match the >> definition for those terms, and provided they give some metadata >> for other elements. Possible forms include: >> a. A completely hierarchical, ABCD-like, XML representation >> b. A completely flat denormalised, simple-DwC-like, CVS >> representation, if the data includes no elements with higher >> cardinality >> c. A set of flat, relational, CVS representations, as with >> Darwin Core Archive star schemas, but with freedom to have more >> complex graphed relationships as needed It is important to limit the set of acceptable formats, and develop tools for interconversion among those formats. >> 9. Each table of CVS data in 8b and 8c is a view that >> corresponds to a linear subgraph of the TDWG ontology, identified >> by the classes of the DwC properties used ? this allows us to >> infer the ?shape? of the data in terms of the ontology If all DwC terms were classes or properties (depending on which was more relevant) in an ontology, the graph could be inferred automatically. There are already tools for converting tabular ontology-tagged data into an ontology graph. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden On Mon, Oct 14, 2013 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 > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-content > or, via email, send a message with subject or body 'help' to > tdwg-content-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-content-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-content digest..." > > > Today's Topics: > > 1. Re: A plea around basisOfRecord (Was: Proposed new Darwin > Core terms - abundance, abundanceAsPercent) (Steve Baskauf) > 2. Re: A plea around basisOfRecord (Was: Proposed new Darwin > Core terms - abundance, abundanceAsPercent) (Steve Baskauf) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 13 Oct 2013 17:13:58 -0500 > From: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> > Subject: Re: [tdwg-content] A plea around basisOfRecord (Was: Proposed > new Darwin Core terms - abundance, abundanceAsPercent) > To: Robert Guralnick <Robert.Guralnick(a)colorado.edu> > Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> > Message-ID: <525B1B26.1010806(a)vanderbilt.edu> > Content-Type: text/plain; charset="windows-1252" > > Sorry, I don't agree at all. > > The core Darwin-SW classes include only Darwin Core classes and the two > proposed DwC classes (Organism and CollectionObject a.k.a. > dsw:IndividualOrganism and dsw:Evidence) which underwent 30 day public > comment period [1] and were submitted to the Executive which recommended > further consideration by the RDF Task Group and the community at large. > The Documenting Darwin Core sessions at the TDWG meeting will pick up > these and other open issues for further discussion and hopefully move > them towards closure one way or the other. If the two proposed classes > are at some point accepted for inclusion in DwC, Darwin-SW will use the > new classes and deprecate dsw:IndividualOrganism and dsw:Evidence, > leaving only Darwin Core classes as the core classes in Darwin-SW. > > It is NOT my view that Darwin-SW is unable to handle current needs for > linking resources effectively. If anyone wants to know why I say that, > come to our talk in the Friday 9AM session on Ontologies and Formal > Models at the meeting. We will show how real SPARQL queries on > Darwin-SW-based data can address important competency questions > involving diverse linked resources. Or see me any time during the > meeting earlier in the week and I'll be happy to give you a personal > demonstration not limited to 9 minutes. > > Steve > > [1] > http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html > see also open issue > https://code.google.com/p/darwincore/issues/detail?id=69 > > > > > Robert Guralnick wrote: > > > > Rod --- There are a couple different conceptions of > > interrelationships between Darwin Core "classes", including the Darwin > > Core Semantic Web effort led by Steve Baskauf and Cam Web, and the > > BiSciCol project. Darwin Core SW is > > here: https://code.google.com/p/darwin-sw/ and the BiSciCol "take" is > > here: http://biscicol.blogspot.com/2013_03_01_archive.html. The > > Darwin Core SW version includes new classes not in Darwin Core, while > > BiSciCol uses only existing class terms and a very simple set of > > predicates. > > > > I think in many people's view, including those of the authors of the > > above (although I hate speaking for them), neither DW-SW or > > DW-BiSciCol may be really able to handle the current needs for linking > > resources together effectively. There has been a major effort to > > refocus away from jury-rigging Darwin Core to try to serve in a more > > semantic framework and pushing towards other solutions that align > > biodiversity standards more with the OBO Foundry > > (http://www.obofoundry.org/) The Biocollections Ontology > > (BCO; https://code.google.com/p/bco/) represents (what I hope) is a > > clear rethinking of the challenge that does connect back to the Darwin > > Core. > > > > Best, Rob > > > > > > > > On Sun, Oct 13, 2013 at 1:52 PM, Roderic Page <r.page(a)bio.gla.ac.uk > > <mailto:r.page@bio.gla.ac.uk>> wrote: > > > > I've always been somewhat puzzled by the disconnect between the > > TDWG LSID ontology > > (e.g., http://rs.tdwg.org/ontology/voc/TaxonConcept ) which has a > > rich set of classes and links between those classes, and Darwin > > Core > > (e.g., http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm ) > > which overlaps with this vocabulary and, in my opinion, does a > > worse job in some areas, notably taxon names and concepts. Maybe > > the LSID vocabulary suffered from the limited uptake of LSIDs > > (apart from the nomenclators and Catalogue of Life) or from the > > complexity of dealing with RDF, but it seems that much of the > > essential work was done when Roger Hyam created that ontology. > > > > What might help is a way to visualise the TDWG LSID ontology in > > terms of the interconnections between the different classes. I'm > > not aware of such a visualisation (nor of an equivalent one for > > the Darwin Core classes). > > > > In any event, it seems odd to have two distinct ontologies that > > are both in use, and which overlap so significantly. > > > > Regards > > > > Rod > > On 13 Oct 2013, at 16:12, Donald Hobern [GBIF] wrote: > > > >> It?s been a couple of weeks but I said I?d try to write something > >> about a more general concern I have around the way we use > >> basisOfRecord and dcterms:type to hold values like occurrence, > >> event and materialSample. This is something that has concerned > >> me for years and that, I worry, is making everything we all do > >> much messier than it need be. > >> > >> I believe that the way we have come to use Darwin Core > >> basisOfRecord is confused and unhelpful. I really wish we used > >> Darwin Core like this: > >> > >> 1. basisOfRecord should be used ONLY to indicate the type > >> of evidence that lies behind a record ? a key aspect of whether > >> the record is likely to be useful for different purposes > >> 2. basisOfRecord values should be taken from a hierarchical > >> vocabulary with three main branches: > >> a. ?specimens? (i.e. biological material that can be > >> reviewed), with a hierarchy of subordinate values such as > >> ?pinnedSpecimen?, ?herbariumSheet?, etc. > >> b. derived, non-biological evidence (not sure what name), > >> with a hierarchy of subordinate values such as ?dnaSequence?, > >> ?soundRecording?, ?stillImage?, etc. > >> c. asserted observations with no revisitable evidence other > >> than the authority of the observer > >> 3. TDWG should deliver a basic ontology in the form of a > >> graph of key relationships between the most significant > >> conceptual entities in our world (TaxonName, TaxonConcept, > >> Identification, Collection, Specimen, Locality, Agent, ?) > >> 4. This ontology should not attempt to map all the > >> complexity of biodiversity-related data ? just provide the > >> high-level map and key relationships (TaxonConcept hasName > >> TaxonName, Specimen heldIn Collection, etc.) ? it should leave > >> definition of other properties as a separate, open-ended activity > >> for the community > >> 5. This ontology should be reviewed at regular intervals > >> and versioned as necessary to address critical gaps ? provided > >> that backwards compatibility is maintained (splitting a class > >> into multiple consitituent classes probably won?t break anything, > >> so start simple) > >> 6. The Darwin Core vocabulary should be published as a > >> flat, open-ended list of terms with clear definitions that can be > >> freely combined as columns in denormalised records > >> 7. Every Darwin Core term should be documented to be > >> tightly associated with a single, fixed class in the ontology > >> (e.g. scientificName and specificEpithet are ALWAYS considered to > >> be properties of a TaxonName whether or not that TaxonName object > >> is clearly referenced or separated out) > >> 8. Every data publisher should be encouraged to share all > >> relevant data elements in their source data in the most > >> convenient normalised or denormalised form, provided they use the > >> recognised Darwin Core properties for elements that match the > >> definition for those terms, and provided they give some metadata > >> for other elements. Possible forms include: > >> a. A completely hierarchical, ABCD-like, XML representation > >> b. A completely flat denormalised, simple-DwC-like, CVS > >> representation, if the data includes no elements with higher > >> cardinality > >> c. A set of flat, relational, CVS representations, as with > >> Darwin Core Archive star schemas, but with freedom to have more > >> complex graphed relationships as needed > >> 9. Each table of CVS data in 8b and 8c is a view that > >> corresponds to a linear subgraph of the TDWG ontology, identified > >> by the classes of the DwC properties used ? this allows us to > >> infer the ?shape? of the data in terms of the ontology > >> 10. If we do this, we do not need to worry about whether a > >> record is a checklist record, an event, an occurrence, a material > >> sample or whatever else, although we could use the dcterms: type > >> property, or some new property, to hold this detail as a further > >> clue to intent and possible use for the record > >> > >> Here is an example. In today?s terms, what sort of DwC record is > >> this? Do I really have to replace ?recordId? with ?eventId?, > >> ?occurrenceId? or similar? And which should I choose? > >> > >> *recordId, decimalLatitude, decimalLongitude, > >> coordinatePrecision, eventDate, scientificName, individualCount* > >> > >> I think it is clear that this record tells us that there was a > >> recording event at a particular time and place where someone or > >> some process recorded a given number of individual organisms > >> which were identified as representatives of a taxon concept with > >> a name corresponding to the supplied scientific name. In other > >> words this gives us some properties from a subgraph that might > >> include, say, instances of TDWG Event, Locality, Date, > >> Occurrence, Identification, TaxonConcept and TaxonName classes. > >> None of these is specifically referenced but we can unambiguously > >> fold the flat record onto the ontology. We can moreover then use > >> the combination of supplied elements to decide whether this > >> record would be of interest to GBIF, a national information > >> facility, a tool cataloguing uses of scientific names, etc. The > >> same will also apply if multiple CVS tables are provided as in 8c. > >> > >> I have thought about this for a long time and cannot yet think of > >> an area in which this would not work efficiently ? and > >> unambiguously ? for all concerned. There are some cases where > >> multiple instances of the same ontology class would be referenced > >> within a single record, which may mean more care is needed by the > >> publisher (e.g. if an insect specimen record includes a reference > >> to a host plant). There may be cases where automated review of > >> the data indicates that there are impossible combinations or > >> ambiguities that the publisher must resolve. However I believe > >> we could use this approach to generalise all mobilisation and > >> consumption of biodiversity data (including all the things we > >> have addressed under ABCD, SDD, TCS, Plinian Core, etc.) and to > >> make it genuinely possible for any data holder to share all the > >> data they have in a form that makes sense to them, while allowing > >> others to consume these data intelligently. > >> > >> Right now, I think our confused use of basisOfRecord is almost > >> the only thing that stops us from exploring this. We have > >> blurred the question of the evidence for a record, with the > >> question of the ?shape? of the record as a subgraph. These are > >> different things. Separating them will allow us to get away from > >> some of our unresolvable debates and open up the doors to much > >> simpler data sharing and reuse. > >> > >> Thanks, > >> > >> Donald > >> > >> > ---------------------------------------------------------------------- > >> Donald Hobern - GBIF Director - dhobern(a)gbif.org > >> <mailto:dhobern@gbif.org> > >> Global Biodiversity Information Facility http://www.gbif.org/ > >> GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?, > >> Denmark > >> Tel: +45 3532 1471 <tel:%2B45%203532%201471> Mob: +45 2875 1471 > >> <tel:%2B45%202875%201471> Fax: +45 2875 1480 > >> <tel:%2B45%202875%201480> > >> > ---------------------------------------------------------------------- > >> _______________________________________________ > >> tdwg-content mailing list > >> tdwg-content(a)lists.tdwg.org <mailto:tdwg-content@lists.tdwg.org> > >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > --------------------------------------------------------- > > Roderic Page > > Professor of Taxonomy > > Institute of Biodiversity, Animal Health and Comparative Medicine > > College of Medical, Veterinary and Life Sciences > > Graham Kerr Building > > University of Glasgow > > Glasgow G12 8QQ, UK > > > > Email: r.page(a)bio.gla.ac.uk <mailto:r.page@bio.gla.ac.uk> > > Tel: +44 141 330 4778 <tel:%2B44%20141%20330%204778> > > Fax: +44 141 330 2792 <tel:%2B44%20141%20330%202792> > > Skype: rdmpage > > Facebook: http://www.facebook.com/rdmpage > > LinkedIn: http://uk.linkedin.com/in/rdmpage > > Twitter: http://twitter.com/rdmpage > > Blog: http://iphylo.blogspot.com > > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > > Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page > > Citations: > > http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ > > <http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ> > > ORCID: http://orcid.org/0000-0002-7101-9767 > > > > > > _______________________________________________ > > tdwg-content mailing list > > tdwg-content(a)lists.tdwg.org <mailto:tdwg-content@lists.tdwg.org> > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > -- > 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 > >

2 1

A plea around basisOfRecord (Was: Proposed new Darwin Core terms - abundance, abundanceAsPercent)
by Donald Hobern [GBIF] 15 Oct '13

15 Oct '13

Its been a couple of weeks but I said Id try to write something about a more general concern I have around the way we use basisOfRecord and dcterms:type to hold values like occurrence, event and materialSample. This is something that has concerned me for years and that, I worry, is making everything we all do much messier than it need be. I believe that the way we have come to use Darwin Core basisOfRecord is confused and unhelpful. I really wish we used Darwin Core like this: 1. basisOfRecord should be used ONLY to indicate the type of evidence that lies behind a record a key aspect of whether the record is likely to be useful for different purposes 2. basisOfRecord values should be taken from a hierarchical vocabulary with three main branches: a. specimens (i.e. biological material that can be reviewed), with a hierarchy of subordinate values such as pinnedSpecimen, herbariumSheet, etc. b. derived, non-biological evidence (not sure what name), with a hierarchy of subordinate values such as dnaSequence, soundRecording, stillImage, etc. c. asserted observations with no revisitable evidence other than the authority of the observer 3. TDWG should deliver a basic ontology in the form of a graph of key relationships between the most significant conceptual entities in our world (TaxonName, TaxonConcept, Identification, Collection, Specimen, Locality, Agent, ) 4. This ontology should not attempt to map all the complexity of biodiversity-related data just provide the high-level map and key relationships (TaxonConcept hasName TaxonName, Specimen heldIn Collection, etc.) it should leave definition of other properties as a separate, open-ended activity for the community 5. This ontology should be reviewed at regular intervals and versioned as necessary to address critical gaps provided that backwards compatibility is maintained (splitting a class into multiple consitituent classes probably wont break anything, so start simple) 6. The Darwin Core vocabulary should be published as a flat, open-ended list of terms with clear definitions that can be freely combined as columns in denormalised records 7. Every Darwin Core term should be documented to be tightly associated with a single, fixed class in the ontology (e.g. scientificName and specificEpithet are ALWAYS considered to be properties of a TaxonName whether or not that TaxonName object is clearly referenced or separated out) 8. Every data publisher should be encouraged to share all relevant data elements in their source data in the most convenient normalised or denormalised form, provided they use the recognised Darwin Core properties for elements that match the definition for those terms, and provided they give some metadata for other elements. Possible forms include: a. A completely hierarchical, ABCD-like, XML representation b. A completely flat denormalised, simple-DwC-like, CVS representation, if the data includes no elements with higher cardinality c. A set of flat, relational, CVS representations, as with Darwin Core Archive star schemas, but with freedom to have more complex graphed relationships as needed 9. Each table of CVS data in 8b and 8c is a view that corresponds to a linear subgraph of the TDWG ontology, identified by the classes of the DwC properties used this allows us to infer the shape of the data in terms of the ontology 10. If we do this, we do not need to worry about whether a record is a checklist record, an event, an occurrence, a material sample or whatever else, although we could use the dcterms: type property, or some new property, to hold this detail as a further clue to intent and possible use for the record Here is an example. In todays terms, what sort of DwC record is this? Do I really have to replace recordId with eventId, occurrenceId or similar? And which should I choose? recordId, decimalLatitude, decimalLongitude, coordinatePrecision, eventDate, scientificName, individualCount I think it is clear that this record tells us that there was a recording event at a particular time and place where someone or some process recorded a given number of individual organisms which were identified as representatives of a taxon concept with a name corresponding to the supplied scientific name. In other words this gives us some properties from a subgraph that might include, say, instances of TDWG Event, Locality, Date, Occurrence, Identification, TaxonConcept and TaxonName classes. None of these is specifically referenced but we can unambiguously fold the flat record onto the ontology. We can moreover then use the combination of supplied elements to decide whether this record would be of interest to GBIF, a national information facility, a tool cataloguing uses of scientific names, etc. The same will also apply if multiple CVS tables are provided as in 8c. I have thought about this for a long time and cannot yet think of an area in which this would not work efficiently and unambiguously for all concerned. There are some cases where multiple instances of the same ontology class would be referenced within a single record, which may mean more care is needed by the publisher (e.g. if an insect specimen record includes a reference to a host plant). There may be cases where automated review of the data indicates that there are impossible combinations or ambiguities that the publisher must resolve. However I believe we could use this approach to generalise all mobilisation and consumption of biodiversity data (including all the things we have addressed under ABCD, SDD, TCS, Plinian Core, etc.) and to make it genuinely possible for any data holder to share all the data they have in a form that makes sense to them, while allowing others to consume these data intelligently. Right now, I think our confused use of basisOfRecord is almost the only thing that stops us from exploring this. We have blurred the question of the evidence for a record, with the question of the shape of the record as a subgraph. These are different things. Separating them will allow us to get away from some of our unresolvable debates and open up the doors to much simpler data sharing and reuse. Thanks, Donald ---------------------------------------------------------------------- Donald Hobern - GBIF Director - <mailto:dhobern@gbif.org> dhobern(a)gbif.org Global Biodiversity Information Facility <http://www.gbif.org/> http://www.gbif.org/ GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480 ----------------------------------------------------------------------

6 13

primer video for Semantics of Biodiversity Symposium
by Steve Baskauf 15 Oct '13

15 Oct '13

The Semantics for Biodiversity symposium at the TDWG Annual Conference has three sessions devoted to presentations related to use of semantic technologies in a biodiversity context. A fourth session [1], which will occur first chronologically, is a primer session intended to provide attendees with the background needed to understand the content of the three later sessions. The primer session assumes a familiarity with basic terminology used in Resource Description Framework (such as URI, triple, subject, predicate, object, property, namespace, value, graph, node, serialization). If you are not already familiar with these terms, there is an 18 minute video geared towards beginners that explains these terms and shows how RDF is presented in its most user-friendly form (Turtle serialization). The video can be watched at http://youtu.be/XAGifYBiXMY . Additional background information is available on the RDF Task Group's website. [2]. Have fun! Steve Baskauf [1] https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/paper/view/448 [2] http://code.google.com/p/tdwg-rdf/wiki/Beginners -- 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

1 0

Delimiters for Darwin Core list-type terms
by John Wieczorek 10 Oct '13

10 Oct '13

Dear all, On the list of pending Darwin Core issues is a topic of general concern about terms that could or do recommend the concatenation and delimiting of a list of values. The specific issue was submitted on the Darwin Core Project site at https://code.google.com/p/darwincore/issues/detail?id=168. Right now there is variation in the recommendations of distinct terms. The Darwin Core terms that could be used to hold lists include the following (use the index at http://rs.tdwg.org/dwc/terms/index.htm#theterms to find and see the details of each of these): informationWithheld dataGeneralizations dynamicProperties recordedBy preparations otherCatalogNumbers previousIdentifications associatedMedia associatedReferences associatedOccurrences associatedSequences associatedTaxa higherGeography georeferenceSources typeStatus higherClassification vernacularName There are some issues. Many terms do not show examples. Most of those that do show examples recommend semi-colon (';') - associatedOccurrences, recordedBy, preparations, otherCatalogNumbers, previousIdentifications, higherGeography, georeferenceSources, and higherClassification, The example for higherClassification does not have spaces after the semi-colon while all others do. Terms that could hold a list of URLs would require a delimiter that would be an invalid part of a URL unless it was escaped. This precludes comma (','), semi-colon (';'), and colon (':'), among others. One possibility here might be the vertical bar or "pipe" ('|'). The term dynamicProperties is meant to take key-value pairs. The examples suggest the format key=value, with any list delimited by a semi-colon, for example, "tragusLengthInMeters=0.014; weightInGrams=120". The example for associatedTaxa also shows a key-value pair ("host: Quercus alba"), but it is formatted differently from the examples for dynamicProperties. There are other terms, such as vernacularName, which could potentially also take a key-value pair, though it is not currently recommended to be a list. Please ignore the issue of whether the idea of list-type terms is a good idea or not - that is not the issue we're trying to resolve here. Instead, the issue is whether a consistent recommendation can be made for how to delimit the values in a list. And if not a consistent recommendation, can we make specific recommendations for distinct terms? If specific recommendations can be made for a term, should that be reflected in examples within the term definitions, or should such recommendations reside only in Type 3 supplementary documentation such as that which can be found on the Darwin Core Project site at, for example, https://code.google.com/p/darwincore/wiki/Occurrence#associatedSequences? Should some of these terms have specific recommendations to contain only single values (e.g., vernacularName), in which case they are not really viable in Simple Darwin Core? Cheers, John

11 26

Re: [tdwg-content] Proposed new Darwin Core environmental terms from ENVO
by Ramona Walls 03 Oct '13

03 Oct '13

Steve and others: The better solution (from an informatics point of view) would be to use the ENVO URI in the field, even if that means changing the DwC guidelines. If it is left as a string, then there would have to be another field that specifies where the term came from, then there would have to be some mechanism to convert the string to a URI. I realize that entering URIs requires some effort, but if someone is looking up the exact label for a term, it is not much harder to find the URI. Re. adding a term to DwC for ecoregion, I suggest you take that up on the ENVO list first. I don't know if they have considered adding a class for ecoregion. To me it makes sense to first work out the utility,definition, and classes in ENVO before adoption in DwC. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Laboratory Research Associate, New York Botanical Garden On Thu, Oct 3, 2013 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 > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-content > or, via email, send a message with subject or body 'help' to > tdwg-content-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-content-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-content digest..." > > > Today's Topics: > > 1. Re: Proposed new Darwin Core environmental terms from ENVO > (Steve Baskauf) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Oct 2013 09:12:54 -0500 > From: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> > Subject: Re: [tdwg-content] Proposed new Darwin Core environmental > terms from ENVO > To: <tuco(a)berkeley.edu> > Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> > Message-ID: <524C29E6.8030908(a)vanderbilt.edu> > Content-Type: text/plain; charset="iso-8859-1" > > John, > > Thank you for your response. I agree that anything that may change over > time should probably be grouped under Event. I guess in the case of > biomes I am thinking about this in a practical sense, i.e. realistically > how is somebody going to assign a particular event to a biome? A likely > scenario would be that they would take the location of an event, use its > latitude and longitude to find where it falls on a map such as > http://en.wikipedia.org/wiki/Biome#Map_of_biomes and then assign it to > whatever biome region it falls within on the map. That is a different > approach from assessing the biological and climatological > characteristics occurring at an event, comparing it with an ontology > that defines biomes, and then making the assignment based on how the > event lines up with the ontology. I suppose that in theory people might > do that, but realistically, it seems more likely that they would look it > up on a map. Under the scenario that they look it up on a map, it is > logical to consider biome to be a property of a location. Yes, biomes > might change over time, but then so do the names and boundaries of > countries, but we don't consider them to be properties of Event, we > consider them as properties of Location. We periodically update the > maps of countries, just as we might update the maps of biomes once a > century or so. But if there is a consensus that dwc:biome belongs under > Event, I can live with it. > > The other thing I'm wondering about the values of dwc:biome would be how > a user would indicate the controlled vocabulary one is using. The ENVO > ontology is mentioned. Under the scenario of the draft RDF guide, the > term dwcuri:biome would have a URI value of > <http://purl.obolibrary.org/obo/ENVO_01000195>. That would be > unambiguous. However, if dwc:biome is reserved for literal values (as > the RDF guide suggests it should be) then how does a machine know that > "flooded grassland biome" is a label from ENVO and not a literal > description of a biome from the Whittaker, Walter, Bailey, etc. systems > which are probably currently in much wider use than ENVO and therefore > likely controlled vocabularies of choice for many users? > > As far as dwc:ecoregion as a term is concerned, I was mostly just > testing the waters. I could submit it as a term addition in the DwC > issue tracker, but I'm not going to do that if I'm the only person who > cares about it. If anybody besides me cares, they can say so on the list. > > Thanks for clarifying, > Steve > > John Wieczorek wrote: > > It is true that the organizedInClass attribute of any given Darwin > > Core term does nothing more than associate properties with classes as > > an organizational aid. It says nothing about the class being the > > domain of the property, and with good reason. Darwin Core in its > > current manifestation is just not semantically detailed enough to make > > domain declarations. Most of our classes combine multiple concepts and > > get used in multiple ways. Occurrence is the best worst example of this. > > > > The environment properties are organized under Event because of their > > time-dependent nature - habitats and biomes definitely can change over > > museum time scales. Location alone does not have a time component - > > the definition of Location is "A spatial region or named place. For > > Darwin Core, a set of terms describing a place, whether named or > > not." Darwin Core has no other spatiotemporal concept except the > > Event, which combines everything in Location with time properties and > > sampling properties - the definition of an Event is: "The category of > > information pertaining to an event (an action that occurs at a place > > and during a period of time)." > > > > If we had a purely spatiotemporal class, then I would organize the > > environmental properties there. Without one, I would organize the > > properties in the class that does have time properties, namely Event. > > > > Until your message, no one has discussed the addition of an ecoregion > > term on tdwg-content. > > > > As to the question of country, I see > > On Tue, Oct 1, 2013 at 5:24 PM, Steve Baskauf > > <steve.baskauf(a)vanderbilt.edu> wrote: > > > I've had some time to read through the proposed changes more closely > > and had > > > a question. > > > > > > I realize that when a property is listed under a class in the dwc: > > > namespace, that is kind of a suggestion about the type of resource > > for which > > > that term would be an appropriate property (vs. a formal domain > > declaration > > > which would force the subject resource to BE an instance of that > > class). So > > > one doesn't really "break the rules" if one uses a DwC term as a > > property of > > > a resource that isn't a member of the class that the term is listed > > under. > > > Nevertheless, for the sake of consistency and to make it possible for > > > consuming applications to know what to "expect" as properties for > > particular > > > types of things, it would be good to place DwC properties under the > > "right" > > > class headings. > > > > > > So my question is, why are the terms dwc:habitat and dwc:biome being > > placed > > > under the dwc:Event class? I'll start with dwc:biome because that's > the > > > most straightforward one. It seems to me that dwc:biome should be > > organized > > > under the class dcterms:Location rather than dwc:Event. For example, I > > > would say > > > > > > <http://bioimages.vanderbilt.edu/baskauf/d0127#loc> dwc:biome > "temperate > > > broadleaf forest" > > > > > > (where http://bioimages.vanderbilt.edu/baskauf/d0127#loc is a > > > dcterms:Location) or something like that. Although I suppose over time > > > climate change could cause that location to be part of a different > > biome, > > > that probably wouldn't happen on a timescale the would be relevant. > One > > > could probably also make the case that dwc:habitat is a property of a > > > location, although I suppose that the habitat type of a location could > > > change, for example if it were a forest, but then somebody chopped > > down all > > > of the trees and converted it to agricultural use. In that case, it > > might > > > be desirable to record what the state of that location was at a > > particular > > > time (which is the way I think about dwc:Event - something that > > happens at a > > > particular place and time). Then it would make sense to group it under > > > dwc:Event. But we have other properties of location that could > > change over > > > time, such as dwc:country for which we have several examples in Europe > > > within the past few decades. > > > > > > I suppose the thinking is that the proposed terms (habitat, biome, > > > environmentalFeature, environmentalMaterial) would comprise a set of > > > properties that would be associated with a collecting or sampling > event. > > > But it doesn't really make sense to me to call dwc:biome a property > > of an > > > event. > > > > > > I'm also wondering if there was any consideration about creating a > > > dwc:ecoregion property, which I would consider to be something > > intermediate > > > in scale between a biome and a habitat. I would actually use that > > term a > > > lot, but I may be the only one (and I would use it as a property of a > > > location). If one were to create such a term, it would probably be > > good to > > > have some other term that specified the system used to define the > > controlled > > > vocabulary (e.g. Bailey vs. WWF ecoregions). Or use URIs but that's a > > > different issue and the DwC RDF guide would have a solution for that > > > (dwcuri:biome, dwcuri:ecoregion, etc.). > > > > > > Steve > > > > > > John Wieczorek wrote: > > > > > > Dear all, > > > > > > The spirit of the proposal is to satisfy use cases defined in the > > > document "Meeting Report: GBIF hackathon-workshop on > > > Darwin Core and sample data (22-24 May 2013)" found at > > > http://www.gbif.org/orc/?doc_id=5424 by reusing terms from the ENVO > > > ontology. Steve is correct. All of the ENVO terms are classes in > > > keeping with the OBO Foundry way of doing things. As such, they don't > > > work in the intended Darwin Core context as they currently stand, > > > where what we want are properties whose values can come from ENVO as a > > > controlled vocabulary in the way Hilmar described. > > > > > > To satisfy the spirit of the proposal, I suggest that instead of > > > replacing the dwc:habitat property with the envo:habitat class and > > > adding the other three ENVO classes, we modify the existing > > > dwc:habitat property and introduce new properties whose ranges are > > > recommended to be the appropriate ENVO classes, as follows: > > > > > > Retain the property term dwc:habitat, but amend the definition to be: > > > > > > Term Name: habitat > > > Identifier: http://rs.tdwg.org/dwc/terms/habitat > > > Namespace: http://rs.tdwg.org/dwc/terms/ > > > Label: Habitat > > > Definition: A spatial region having environmental qualities which may > > > sustain an organism or a community of organisms. Recommended best > > > practice is to use a controlled vocabulary such as defined by the > > > habitat class of the Environment Ontology (ENVO). > > > Comment: Examples: "freshwater habitat", > > > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > > Refines: > > > Status: proposed > > > Date Issued: 2008-11-19 > > > Date Modified: 2013-09-26 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: habitat-2013-09-26 > > > Replaces: habitat-2009-04-24 > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Add the following new property terms for biome, > > > environmental feature, and environmental material: > > > > > > Term Name: biome > > > Identifier: http://rs.tdwg.org/dwc/terms/biome > > > Namespace: http://rs.tdwg.org/dwc/terms/ > > > Label: Biome > > > Definition: A major class of ecologically similar communities of > > > plants, animals, and other organisms. Biomes are defined based on > > > factors such as plant structures (such as trees, shrubs, and grasses), > > > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > > > woodland, savanna), and other factors like climate. Unlike ecozones, > > > biomes are not defined by genetic, taxonomic, or historical > > > similarities. Biomes are often identified with particular patterns of > > > ecological succession and climax vegetation. Recommended best practice > > > is to use a controlled vocabulary such as defined by the biome class > > > of the Environment Ontology (ENVO). > > > Comment: Examples: "flooded grassland biome", > > > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-26 > > > Date Modified: 2013-09-26 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: biome-2013-09-26 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Term Name: environmentalFeature > > > Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature > > > Namespace: http://rs.tdwg.org/dwc/terms/ > > > Label: Environmental Feature > > > Definition: A prominent or distinctive aspect, quality, or > > > characteristic of a biome. Recommended best practice is to use a > > > controlled vocabulary such as defined by the environmental feature > > > class of the Environment Ontology (ENVO). > > > Comment: Examples: "meadow", > > > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-26 > > > Date Modified: 2013-09-26 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: environmentalFeature-2013-09-26 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Term Name: environmentalMaterial > > > Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial > > > Namespace: http://rs.tdwg.org/dwc/terms/ > > > Label: Environmental Material > > > Definition: Material in or on which organisms may live. Recommended > > > best practice is to use a controlled vocabulary such as defined by the > > > environmental feature class of the Environment Ontology (ENVO). > > > Comment: Examples: "scum", > > > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-26 > > > Date Modified: 2013-09-26 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: environmentalMaterial-2013-09-26 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > I hope this makes better sense. > > > > > > Cheers, > > > > > > John > > > > > > On Thu, Sep 26, 2013 at 4:03 AM, Steve Baskauf > > > <steve.baskauf(a)vanderbilt.edu> wrote: > > > > > > > > > Well, the proposal says "The Darwin Core term habitat would be > > redefined..." > > > . I take that to mean that the term dwc:habitat is being replaced with > > > envo:00002036 . If that's not what it means, then it would be good to > > > clarify. If the intention is to provide values for other terms, > > that should > > > be stated. > > > > > > Steve > > > > > > > > > Hilmar Lapp wrote: > > > > > > I was assuming that the proposal was that subclasses of envo:habitat > > would > > > take the place of values for the dwc:habitat property. But perhaps I > was > > > naive or misunderstanding? > > > > > > -hilmar > > > > > > Sent from away > > > > > > On Sep 25, 2013, at 8:23 PM, Steve Baskauf > > <steve.baskauf(a)vanderbilt.edu> > > > wrote: > > > > > > OK, now that I've had a chance to look at the RDF, it is as I > > suspected. If > > > I am understanding the proposal correctly, the proposal is to > > replace the > > > term <http://rs.tdwg.org/dwc/terms/habitat> (i.e. dwc:habitat) with > > the term > > > <http://purl.obolibrary.org/obo/ENVO_00002036> (which I'll call > > > envo:00002036 for brevity) However, the definition of dwc:habitat > > which you > > > can view at > > > > http://code.google.com/p/darwincore/source/browse/trunk/rdf/dwcterms.rdf > > > says > > > > > > dwc:habitat rdf:type rdfs:Property > > > > > > whereas the document I received at the end of those four redirects > > tells me > > > that > > > > > > envo:00002036 rdf:type owl:Class > > > > > > Since > > > > > > owl:Class rdfs:subclassOf rdfs:Class > > > > > > then we are effectively changing the current DwC "habitat" term from a > > > property into a class similar to dwc:Occurrence, dwc:Identification, > > > dwc:Taxon, etc. which are all of type rdfs:Class. > > > > > > So I'm left wondering what I can do with the new term. With the old > > term I > > > could make a statement like > > > > > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> dwc:habitat > > "deciduous > > > forest" > > > > > > or something like that if I take the hint from the DwC class > > groupings that > > > dwc:habitat might be a property of dwc:Event instances. But I can't > > > meaningfully say > > > > > > <http://bioimages.vanderbilt.edu/baskauf/50750#eve> envo:00002036 > > > "deciduous forest" > > > > > > That doesn't make any sense because the way I understand RDF, > predicates > > > should be properties, not classes. Even if we weren't talking about > > RDF, > > > I'd still have the same problem (we are changing a property into a > > class) - > > > it's just easier for me to make plain what the issue is by giving RDF > > > examples. So just exactly what can I "do" with envo:00002036 ????? > > > > > > I haven't looked up the RDF for the other proposed terms (too much > > work with > > > the four redirects), but I suspect if I did, I'd find that they are > also > > > classes and not properties. This particular issue is a case of a > > broader > > > issue that I have about OBO-style ontologies. They are great for > > defining > > > how many, many kinds of classes are related to each other. But they > > provide > > > very few properties that could be used as predicates to serve as > > properties > > > of instance data. > > > > > > Steve > > > > > > John Wieczorek wrote: > > > > > > Dear all, > > > > > > GBIF has just published "Meeting Report: GBIF hackathon-workshop on > > > Darwin Core and sample data (22-24 May 2013)" at > > > http://www.gbif.org/orc/?doc_id=5424. Now that this document is > > > available for public reference, I would like to formally open the > > > minimum 30-day comment period on the new environmental terms proposed > > > during the workshop and defined in the referenced document. > > > > > > The formal proposal would change the term habitat to align it with the > > > ENVO habitat term. The related issues in the Darwin Core issue tracker > > > is https://code.google.com/p/darwincore/issues/detail?id=178. The > > > Darwin Core term habitat would be redefined as follows: > > > > > > Term Name: habitat > > > Identifier: http://purl.obolibrary.org/obo/ENVO_00002036 > > > Namespace: http://purl.obolibrary.org/obo/ > > > Label: Habitat > > > Definition: A spatial region having environmental qualities which may > > > sustain an organism or a community of organisms. > > > Comment: Examples: "freshwater habitat", > > > "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > > > Refines: > > > Status: proposed > > > Date Issued: 2008-11-19 > > > Date Modified: 2013-09-25 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: http://purl.obolibrary.org/obo/ENVO_00002036 > > > Replaces: habitat-2009-04-24 > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > The formal proposal would add the following new terms for biome, > > > environmental feature, and environmental material: > > > > > > Term Name: biome > > > Identifier: http://purl.obolibrary.org/obo/ENVO_00000428 > > > Namespace: http://purl.obolibrary.org/obo/ > > > Label: Biome > > > Definition: A major class of ecologically similar communities of > > > plants, animals, and other organisms. Biomes are defined based on > > > factors such as plant structures (such as trees, shrubs, and grasses), > > > leaf types (such as broadleaf and needleleaf), plant spacing (forest, > > > woodland, savanna), and other factors like climate. Unlike ecozones, > > > biomes are not defined by genetic, taxonomic, or historical > > > similarities. Biomes are often identified with particular patterns of > > > ecological succession and climax vegetation. > > > Comment: Examples: "flooded grassland biome", > > > "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-25 > > > Date Modified: 2013-09-25 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: http://purl.obolibrary.org/obo/ENVO_00000428 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Term Name: environmental feature > > > Identifier: http://purl.obolibrary.org/obo/ENVO_00002297 > > > Namespace: http://purl.obolibrary.org/obo/ > > > Label: Environmental Feature > > > Definition: A prominent or distinctive aspect, quality, or > > > characteristic of a biome. > > > Comment: Examples: "meadow", > > > "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-25 > > > Date Modified: 2013-09-25 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: http://purl.obolibrary.org/obo/ENVO_00002297 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > Term Name: environmental material > > > Identifier: http://purl.obolibrary.org/obo/ENVO_00010483 > > > Namespace: http://purl.obolibrary.org/obo/ > > > Label: Environmental Material > > > Definition: Material in or on which organisms may live. > > > Comment: Examples: "scum", > > > "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see > > > http://code.google.com/p/darwincore/wiki/Event (there will be no > > > further documentation here until the term is ratified) > > > Type of Term: http://www.w3.org/2000/01/rdf-schema#Class > > > Refines: > > > Status: proposed > > > Date Issued: 2013-09-25 > > > Date Modified: 2013-09-25 > > > Has Domain: > > > Has Range: > > > Refines: > > > Version: http://purl.obolibrary.org/obo/ENVO_00010483 > > > Replaces: > > > IsReplaceBy: > > > Class: http://rs.tdwg.org/dwc/terms/Event > > > ABCD 2.0.6: not in ABCD (someone please confirm or deny this) > > > > > > The related issues in the Darwin Core issue tracker are > > > https://code.google.com/p/darwincore/issues/detail?id=189 > > > https://code.google.com/p/darwincore/issues/detail?id=190 > > > and > > > https://code.google.com/p/darwincore/issues/detail?id=191 > > > > > > If there are any objections to the changes proposed for these terms, > > > or comments about their definitions, please respond to this message. > > > If there are no objections or if consensus can be reached on any > > > amendments put forward, the proposal will go before the Executive > > > Committee for authorization to put these additions into effect after > > > the public commentary period. > > > > > > Cheers, > > > > > > John > > > _______________________________________________ > > > tdwg-content mailing list > > > tdwg-content(a)lists.tdwg.org > > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > . > > > > > > > > > > > > > > > -- > > > 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 <tel:%28615%29%20343-4582>, fax: (615) > > 322-4942 <tel:%28615%29%20322-4942> > > > If you fax, please phone or email so that I will know to look for it. > > > http://bioimages.vanderbilt.edu > > > > > > > > > _______________________________________________ > > > tdwg-content mailing list > > > tdwg-content(a)lists.tdwg.org > > > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > > > > > > -- > > > 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 <tel:%28615%29%20343-4582>, fax: (615) > > 322-4942 <tel:%28615%29%20322-4942> > > > If you fax, please phone or email so that I will know to look for it. > > > http://bioimages.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 <tel:%28615%29%20343-4582>, fax: (615) > > 322-4942 <tel:%28615%29%20322-4942> > > > If you fax, please phone or email so that I will know to look for it. > > > http://bioimages.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 > >

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