- tdwg-content - lists.tdwg.org

NESCent summer course: "Ontologies for Evolutionary Biology"
by Matt Yoder 31 May '13

31 May '13

Apologies in advance- this is a little off topic but I think it should be of interest to many here. For a second year we are teaching a "Ontologies for Evolutionary Biology" sponsored by NESCent on July 29th in Durham, NC. Details are here: http://bit.ly/ZAQ6Dt . Please forward this to any interested parties. Last year we had a broad spectrum of "students", from advanced undergrads to Professors nearing retirement. If you have questions please message me off-list. Thanks, Matt Yoder Biological Informatician Illinois Natural History Survey

1 0

Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
by Richard Pyle 30 May '13

30 May '13

Hi Ramona, Yes, I agree, and thanks. Ive always felt that there has been a trend towards trying to push too much ontology (or other semantic meaning) onto DWC terms and classes, when DWC was fundamentally intended to represent an mechanism for data exchange; not a mechanism to describe the ontological landscape of biodiversity data. The only reason I brought this up now (and, I think, why we discussed it in 2010), is that the term individualID in DWC sort of hinted that something like Individual was the forgotten class for DWC. I sincerely hope that BCO and DSW gain more traction (and, ideally, harmony between them) than earlier attempts at developing ontologies in this space have met and clearly that is the right path forward. My main concern for this thread (and the reason I engaged in it), was to: 1) Find out the status of the discussions that began in 2010; and 2) Clarify where the current materialSample proposal overlaps, or does not overlap, with that earlier effort. Steve has very adequately answered the first question, and you, John, and others have answered the second, and Im happy with both sets of answers. Im sorry for the voluminous exchange, but I felt the discussion was both important, and very helpful (certainly to me). Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Wednesday, May 29, 2013 1:03 PM To: Richard Pyle Cc: John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Hi Rich, Sorry I didn't mention this sooner, but your emails were also helpful to me in describing an important and generalizable use case. I don't know whether or not the TDWG community is ready to deal with the level of abstraction we are talking about, but my assessment is that whether or not they are ready, the Darwin Core is not constructed to deal with it. That is why (among other reasons) we started work on the BCO, and perhaps one reason why Steve and others developed DSW. Our goal with the material sample proposal was not to overhaul DwC, but to work within the DwC framework to make it more compatible with other standards such as MIxS. That is why we tried to keep our proposal fairly narrowly focused. Ramona On Wed, May 29, 2013 at 3:21 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Thanks, Ramona this is an *extremely* helpful email! It helps clear things up a lot in my mind. Just to be clear, what I am looking for is the notion of a defined physical object (what I think you mean by material entity), and I explicitly mean the material entity itself. Yes, there is information (properties) that relate to that material entity, but to me that is a separate issue. What I would like to see clearly defined is the class representing the material (physical) entity which seems to me to be a superclass of what materialSample is intended to represent. Perhaps our (TDWG/DWC) community is not yet ready to deal with this level of abstraction (unfortunately, I absolutely have to, because Occurrence is simply way too overloaded a class for me to use independently of what I have been calling individual and what I have been calling Evidence). In that case, I guess the best thing to do is accept materialSample as a basisOfRecord for Occurrence and move on. But this is more or less the same thing that happened the last time we engaged in this conversation (2 years or so ago), and I was hoping this conversation about materialSample could leverage progress on the larger issue. As Ive said before, the last thing I want to do is confuse or otherwise slow down the process of incorporating the term materialSample into DWC. Its just that I saw enough overlap with that other issue, that I was hoping we could find a reasonable pathway forward on both. Thanks again for the very helpful comments. Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Wednesday, May 29, 2013 9:14 AM To: Richard Pyle Cc: John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Rich, I now understand more fully what you are asking for ( a clear definition goes a long way!). A material sample, as we discussed it at the Kansas and Oxford workshops, does indeed need to be physically removed from its environment. This is also the case with the OBI term material sample, which, as a subclass of OBI:specimen is the output of some collecting process. It is true that concept of material sample could be defined to include sampling in an observational sense, but that is not how it is defined at this point. Based on this, material sample is NOT the term you are looking for or defined as : "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." What you have defined is a category of information (whatever that may be) that pertains to some material entity. Not the material entity itself, but information about that entity. The "SuperclassTerm" you refer to in the definition sounds an awful lot like a material entity from the Basic Formal Ontology, which is used for defining material sample in OBI and the Bio-collections Ontology. Ramona On Wed, May 29, 2013 at 11:51 AM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Many thanks, John. This is extremely helpful! First of all, in the context of a distinct term for basisOfRecord, I see absolutely no problem with adding the term MaterialSample. I fully support your proposal (although if this is simply a basisOfRecord term to be used alongside Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation; does it need a defined ID term? Do all the others have defined ID terms?). However, Im excited by this conversation because I think we are very close to solving a bigger problem (which was the focus of the 2010 discussion on this list around IndividualOrganism). This bigger problem involves the need for a defined concept (Im hesitating to say class), and an associated ID, in dwc that refers to the physical/material basis of an Occurrence. We dont yet have a term for this concept in dwc (IndividualID hinted at the need for one, but that term was not well-defined, and the term itself seems to cause confusion). As Steve Baskauf and I have both been advocating for the establishment of new class in dwc for exactly this purpose, I just want to make sure that were on the same page about what each concept is. The more I understand about what you need for materalSample, the more convinced I am that both of our needs can be met with the same concept. I am perfectly happy to adopt the term MaterialSample, but I guess it all boils down to this: In order for something to be a MaterialSample, must it necessarily be removed from nature? If the answer is No, then I think we can merge the two concepts into one. If the answer is Yes, then I think materialSample is best characterized as a subclass of what Steve and I have been pushing for (setting aside, for the moment, the additional complexity of taxonomically homogeneous vs. heterogeneous). In the latter case, I would define the superclass (whatever term is used for it), along the lines of: "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." Aloha, Rich From: jdeck88(a)gmail.com [mailto:jdeck88@gmail.com] On Behalf Of John Deck Sent: Wednesday, May 29, 2013 4:01 AM To: Richard Pyle Cc: Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton; Ramona Walls Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Since the original proposal was from a group of folks, we decided to put our heads together to construct a general response to the various issues and ideas expressed on this thread. John Deck for Rob Guralnick, Ramona Walls, and John Wieczorek In the text of the issue submitted for MaterialSample ( <https://code.google.com/p/darwincore/issues/detail?id=167> https://code.google.com/p/darwincore/issues/detail?id=167) we noted cases where the current basisOfRecord terms pertaining to the Occurrence class (Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation) do not adequately cover certain cases, including: environmental sample (for metagenomic analysis), transcriptomes (measuring genes but not taxa), and destructive samples (e.g. tissues destructively sampled in order to generate genomic DNA). The term we borrowed from OBI (http://purl.obolibrary.org/obo/OBI_0000747) is broad enough to be utilized across various cases that fulfill our criteria while still maintaining a consistent, clear and human understandable meaning. For our purposes, we can think of Material Sample as any type of matter that we can use in order derive further evidence needed for identifications, and taxa, whether it is taxonomically homogenous, heterogenous, a single individual, sets of individuals, or populations. How is MaterialSample different from Individual? The intent of individualID is fairly clear: since an Occurrence represents an organism at a place and time (per Markus email), the individualID term allows us to assign an instance identifier for a particular organism that can be present in multiple events. MaterialSampleID, on the other hand, is intended to allow users to say that the basis of an occurence is a material entity (i.e. matter) that has been sampled according to some particular method. Whether or not this material entity is an individual (sensu individualID in DwC) is an independent axis of classification. As was already pointed out, there is no restriction on specifying that an occurence is associated with more than one type, so any occurrence can have both an individualID and a materialSampleID. We maintain our position on the proposal for MaterialSample as a value for the basisOfRecord, with an associated materialSampleID to identify instances of them. Per Steves initial comments, we have already withdrawn the proposal for a MaterialSample class distinct from that in the Darwin Core type vocabulary, which should make it easier to evaluate the implications of what were discussing. ******************** NOTES, MaterialSample from OBI: OBI has fairly broad definitions of samples & specimens that are meant to be utilized across many different scientific activities. Material Sample is defined as a material entity that has the material sample role, while a material sample role is defined as a specimen role borne by a material entity that is the output of a material sampling process, and a material sampling process is a specimen gathering process with the objective to obtain a specimen that is representative of the input material entity. On Mon, May 27, 2013 at 11:59 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hi Markus, Great question! Particularly because this is exactly the sort of use case we designed our model around. > if you take a tissue sample of the same tree every year, would the identifier > in individualID be the same for all of them or be different? WIth the current > dwc:individualID definition it would be the same for all samples. If I > understand you correct each sample would have its own "individual" > identifier in your proposal? It can't see how you can collapse these two things > into one definition. No, that is not how we would handle it. In our model, there would be one IndividualID to represent the tree, spanning the time period beginning (more or less) when the seed was germinated, until the time at which the entire physical structure of the tree was disintegrated. It is an individual tree. There would be multiple Occurrence instances, for each time that someone observed or sampled or otherwise wished to document some condition of that tree. All of these Occurrence instances would refer to the same individualID value (i.e., the "tree"). In the example above, this means there would be a different Occurrence instance for each year that a sample is taken -- because in each case, an assertion that the full tree existed at a certain time and place can be made (I understand that trees tend not to move around very much, so the Location for each event associated with each Occurrence would, in this case, remain the same; but the other Event properties -- such as eventID, samplingProtocol, samplingEffort, eventDate, eventTime, startDayOfYear, endDayOfYear, year, month, day, verbatimEventDate, habitat, fieldNumber, fieldNotes, eventRemarks -- would be documented accordingly for each sampling Occurrence instance). Suppose that the tree is visited every month, but only sampled once per year. In that case, there would be an Occurrence record for every monthly visit. In other words, an Occurrence instance exists regardless of whether a physical sample was made or not. Any in-situ images made of the tree would likewise be associated with the specific Occurrence instance, and each image would represent a separate instance of "Evidence". Now, let's focus on the annual samplings. Every time a new sample is taken from the tree, at least one new instance of Individual (with a unique individualID value) is created to represent the sample. This sample (individual instance) may be a "gathering" (set of multiple individual specimens gathered at the same time), or it may be a single specimen, or it may be simply a tissue sample intended for destructive analysis. In any case, it's a new individual instance derived from the "parent" individual instance representing the whole tree. In our implementation, "Individual" can be hierarchical, such that a whole-organism tree can be sub-sampled with many "child" instances of "gatherings" (say, one gathering each year), and each gathering may have multiple child "specimen" individuals (e.g. individual botanical sheets created from the multiple items of a single gathering), and each specimen may have further "child" subsamples extracted for DNA analysis (or whatever), and the hierarchy can continue on down to whatever derivatives that people feel a need to keep track of (e.g., aliquot). The point is, all Individual instances are well-defined physical objects (or well-defined sets of physical objects), and they can be arranged in a n-tiered hierarchy. Moreover, each Individual that can be characterized as a "sample" (what we refer to as a "CollectionObject") may also have a property value for "CollectionOccurrenceID" -- which refers to the specific Occurrence instance at which the sample was obtained. So, for example, if the tree is visited on May 27, 2013 and a specimen (sample) is taken, then: 1) An Event instance is generated to represent the event where the tree was visited; 2) An Occurrence instance is generated, which refers to the new EventID, and the existing IndividualID for the whole tree, and includes whatever other Occurrence properties are relevant for the tree at the time of this Occurrence 3) An Individual instance is generated for the specimen, which has a property value for parentIndividualID that refers to the individualID for the whole tree, and a property value for collectionOccurrenceID that refers the Occurrence instance where the specimen was collected. So, to summarize the answer to your question: - There are multiple Occurrence instances that refer to the same Individual instance representing the whole tree (and, hence can be collapsed to the same IndividualID value). - Any Individual can have derivatives that are themselves unique Individual instances. - Individuals are arranged hierarchically, and certain properties can be inherited up or down the hierarchy, depending on the properties and their associated logical constraints. At some point, I will assemble a set of other specific use cases, and how we manage them through our use of the "Individual" instance (although I will probably not use the word "Individual", as this seems to cause too much confusion in these discussions). Aloha, Rich -- John Deck (541) 321-0689 <tel:%28541%29%20321-0689>

2 2

Re: [tdwg-content] New Darwin Core terms proposed relating to material samples
by Richard Pyle 29 May '13

29 May '13

Thanks, Ramona this is an *extremely* helpful email! It helps clear things up a lot in my mind. Just to be clear, what I am looking for is the notion of a defined physical object (what I think you mean by material entity), and I explicitly mean the material entity itself. Yes, there is information (properties) that relate to that material entity, but to me that is a separate issue. What I would like to see clearly defined is the class representing the material (physical) entity which seems to me to be a superclass of what materialSample is intended to represent. Perhaps our (TDWG/DWC) community is not yet ready to deal with this level of abstraction (unfortunately, I absolutely have to, because Occurrence is simply way too overloaded a class for me to use independently of what I have been calling individual and what I have been calling Evidence). In that case, I guess the best thing to do is accept materialSample as a basisOfRecord for Occurrence and move on. But this is more or less the same thing that happened the last time we engaged in this conversation (2 years or so ago), and I was hoping this conversation about materialSample could leverage progress on the larger issue. As Ive said before, the last thing I want to do is confuse or otherwise slow down the process of incorporating the term materialSample into DWC. Its just that I saw enough overlap with that other issue, that I was hoping we could find a reasonable pathway forward on both. Thanks again for the very helpful comments. Aloha, Rich From: Ramona Walls [mailto:rlwalls2008@gmail.com] Sent: Wednesday, May 29, 2013 9:14 AM To: Richard Pyle Cc: John Deck; Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Rich, I now understand more fully what you are asking for ( a clear definition goes a long way!). A material sample, as we discussed it at the Kansas and Oxford workshops, does indeed need to be physically removed from its environment. This is also the case with the OBI term material sample, which, as a subclass of OBI:specimen is the output of some collecting process. It is true that concept of material sample could be defined to include sampling in an observational sense, but that is not how it is defined at this point. Based on this, material sample is NOT the term you are looking for or defined as : "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." What you have defined is a category of information (whatever that may be) that pertains to some material entity. Not the material entity itself, but information about that entity. The "SuperclassTerm" you refer to in the definition sounds an awful lot like a material entity from the Basic Formal Ontology, which is used for defining material sample in OBI and the Bio-collections Ontology. Ramona On Wed, May 29, 2013 at 11:51 AM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Many thanks, John. This is extremely helpful! First of all, in the context of a distinct term for basisOfRecord, I see absolutely no problem with adding the term MaterialSample. I fully support your proposal (although if this is simply a basisOfRecord term to be used alongside Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation; does it need a defined ID term? Do all the others have defined ID terms?). However, Im excited by this conversation because I think we are very close to solving a bigger problem (which was the focus of the 2010 discussion on this list around IndividualOrganism). This bigger problem involves the need for a defined concept (Im hesitating to say class), and an associated ID, in dwc that refers to the physical/material basis of an Occurrence. We dont yet have a term for this concept in dwc (IndividualID hinted at the need for one, but that term was not well-defined, and the term itself seems to cause confusion). As Steve Baskauf and I have both been advocating for the establishment of new class in dwc for exactly this purpose, I just want to make sure that were on the same page about what each concept is. The more I understand about what you need for materalSample, the more convinced I am that both of our needs can be met with the same concept. I am perfectly happy to adopt the term MaterialSample, but I guess it all boils down to this: In order for something to be a MaterialSample, must it necessarily be removed from nature? If the answer is No, then I think we can merge the two concepts into one. If the answer is Yes, then I think materialSample is best characterized as a subclass of what Steve and I have been pushing for (setting aside, for the moment, the additional complexity of taxonomically homogeneous vs. heterogeneous). In the latter case, I would define the superclass (whatever term is used for it), along the lines of: "The category of information pertaining to the physical basis of a sampling, subsampling, or observational event. In biological collections, the [SuperclassTerm] is typically a defined group of organisms, a single whole organism, or a part of a whole organism that is collected or otherwise documented in nature, and either preserved, destructively processed, or documented through some form of Evidence (such as images or reported visual observations)." Aloha, Rich From: jdeck88(a)gmail.com [mailto:jdeck88@gmail.com] On Behalf Of John Deck Sent: Wednesday, May 29, 2013 4:01 AM To: Richard Pyle Cc: Markus Döring; Steve Baskauf; TDWG Content Mailing List; Robert Whitton; Ramona Walls Subject: Re: [tdwg-content] New Darwin Core terms proposed relating to material samples Since the original proposal was from a group of folks, we decided to put our heads together to construct a general response to the various issues and ideas expressed on this thread. John Deck for Rob Guralnick, Ramona Walls, and John Wieczorek In the text of the issue submitted for MaterialSample ( <https://code.google.com/p/darwincore/issues/detail?id=167> https://code.google.com/p/darwincore/issues/detail?id=167) we noted cases where the current basisOfRecord terms pertaining to the Occurrence class (Occurrence, PreservedSpecimen, LivingSpecimen, FossilSpecimen, HumanObservation, MachineObservation) do not adequately cover certain cases, including: environmental sample (for metagenomic analysis), transcriptomes (measuring genes but not taxa), and destructive samples (e.g. tissues destructively sampled in order to generate genomic DNA). The term we borrowed from OBI (http://purl.obolibrary.org/obo/OBI_0000747) is broad enough to be utilized across various cases that fulfill our criteria while still maintaining a consistent, clear and human understandable meaning. For our purposes, we can think of Material Sample as any type of matter that we can use in order derive further evidence needed for identifications, and taxa, whether it is taxonomically homogenous, heterogenous, a single individual, sets of individuals, or populations. How is MaterialSample different from Individual? The intent of individualID is fairly clear: since an Occurrence represents an organism at a place and time (per Markus email), the individualID term allows us to assign an instance identifier for a particular organism that can be present in multiple events. MaterialSampleID, on the other hand, is intended to allow users to say that the basis of an occurence is a material entity (i.e. matter) that has been sampled according to some particular method. Whether or not this material entity is an individual (sensu individualID in DwC) is an independent axis of classification. As was already pointed out, there is no restriction on specifying that an occurence is associated with more than one type, so any occurrence can have both an individualID and a materialSampleID. We maintain our position on the proposal for MaterialSample as a value for the basisOfRecord, with an associated materialSampleID to identify instances of them. Per Steves initial comments, we have already withdrawn the proposal for a MaterialSample class distinct from that in the Darwin Core type vocabulary, which should make it easier to evaluate the implications of what were discussing. ******************** NOTES, MaterialSample from OBI: OBI has fairly broad definitions of samples & specimens that are meant to be utilized across many different scientific activities. Material Sample is defined as a material entity that has the material sample role, while a material sample role is defined as a specimen role borne by a material entity that is the output of a material sampling process, and a material sampling process is a specimen gathering process with the objective to obtain a specimen that is representative of the input material entity. On Mon, May 27, 2013 at 11:59 PM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: Hi Markus, Great question! Particularly because this is exactly the sort of use case we designed our model around. > if you take a tissue sample of the same tree every year, would the identifier > in individualID be the same for all of them or be different? WIth the current > dwc:individualID definition it would be the same for all samples. If I > understand you correct each sample would have its own "individual" > identifier in your proposal? It can't see how you can collapse these two things > into one definition. No, that is not how we would handle it. In our model, there would be one IndividualID to represent the tree, spanning the time period beginning (more or less) when the seed was germinated, until the time at which the entire physical structure of the tree was disintegrated. It is an individual tree. There would be multiple Occurrence instances, for each time that someone observed or sampled or otherwise wished to document some condition of that tree. All of these Occurrence instances would refer to the same individualID value (i.e., the "tree"). In the example above, this means there would be a different Occurrence instance for each year that a sample is taken -- because in each case, an assertion that the full tree existed at a certain time and place can be made (I understand that trees tend not to move around very much, so the Location for each event associated with each Occurrence would, in this case, remain the same; but the other Event properties -- such as eventID, samplingProtocol, samplingEffort, eventDate, eventTime, startDayOfYear, endDayOfYear, year, month, day, verbatimEventDate, habitat, fieldNumber, fieldNotes, eventRemarks -- would be documented accordingly for each sampling Occurrence instance). Suppose that the tree is visited every month, but only sampled once per year. In that case, there would be an Occurrence record for every monthly visit. In other words, an Occurrence instance exists regardless of whether a physical sample was made or not. Any in-situ images made of the tree would likewise be associated with the specific Occurrence instance, and each image would represent a separate instance of "Evidence". Now, let's focus on the annual samplings. Every time a new sample is taken from the tree, at least one new instance of Individual (with a unique individualID value) is created to represent the sample. This sample (individual instance) may be a "gathering" (set of multiple individual specimens gathered at the same time), or it may be a single specimen, or it may be simply a tissue sample intended for destructive analysis. In any case, it's a new individual instance derived from the "parent" individual instance representing the whole tree. In our implementation, "Individual" can be hierarchical, such that a whole-organism tree can be sub-sampled with many "child" instances of "gatherings" (say, one gathering each year), and each gathering may have multiple child "specimen" individuals (e.g. individual botanical sheets created from the multiple items of a single gathering), and each specimen may have further "child" subsamples extracted for DNA analysis (or whatever), and the hierarchy can continue on down to whatever derivatives that people feel a need to keep track of (e.g., aliquot). The point is, all Individual instances are well-defined physical objects (or well-defined sets of physical objects), and they can be arranged in a n-tiered hierarchy. Moreover, each Individual that can be characterized as a "sample" (what we refer to as a "CollectionObject") may also have a property value for "CollectionOccurrenceID" -- which refers to the specific Occurrence instance at which the sample was obtained. So, for example, if the tree is visited on May 27, 2013 and a specimen (sample) is taken, then: 1) An Event instance is generated to represent the event where the tree was visited; 2) An Occurrence instance is generated, which refers to the new EventID, and the existing IndividualID for the whole tree, and includes whatever other Occurrence properties are relevant for the tree at the time of this Occurrence 3) An Individual instance is generated for the specimen, which has a property value for parentIndividualID that refers to the individualID for the whole tree, and a property value for collectionOccurrenceID that refers the Occurrence instance where the specimen was collected. So, to summarize the answer to your question: - There are multiple Occurrence instances that refer to the same Individual instance representing the whole tree (and, hence can be collapsed to the same IndividualID value). - Any Individual can have derivatives that are themselves unique Individual instances. - Individuals are arranged hierarchically, and certain properties can be inherited up or down the hierarchy, depending on the properties and their associated logical constraints. At some point, I will assemble a set of other specific use cases, and how we manage them through our use of the "Individual" instance (although I will probably not use the word "Individual", as this seems to cause too much confusion in these discussions). Aloha, Rich -- John Deck (541) 321-0689 <tel:%28541%29%20321-0689>

1 0

Evidence/Token Class [was: New Darwin Core terms proposed relating to material samples]
by Richard Pyle 26 May '13

26 May '13

Thanks, Dan. I changed the subject line because I think your comment: > tissue converted to DNA extract is still tissue (the tissue is still > "material sample" after "destructive sampling", and still part of > the event, just as is a photograph of the beast in the museum. Relates to part of what Steve wrote: > We defined a class for evidence, but we also considered not having evidence > being an explicit class. Not defining an explicit Token class would have simplified > the diagram at the bottom of the page - one could just say that there should be > evidence and it should be linked to the resource it documents. > Token and THeE/IndividualOrganism are not disjoint classes - the physical entity > can be the evidence if somebody "owns" it and makes it available for people to examine. > However, in DSW, Token and THeE are not synonymous because we allow evidence > to include things that are not physically derived from the entity (e.g. images, sounds, > string data records) in addition to physical specimens. This is an area that at first seems subtle, but once we actually started working with data, starts to became more and more intuitive (at least to me, anyway). I first started thinking about this seriously during a 2007 meeting of ICZN Commissioners, when we were contemplating the question of what could/should, and what could/should not, fulfill the role of a type specimen under the ICZN Code. Needless to say, we did not come up with a complete answer to the question, but the discussion did help frame in my mind the question in much better detail. Under the ICZN Code (which differs in a few respects from the ICNafp Code in this area), the definition of a type specimen s fairly straight-forward: 1) It must be biological material. An image (e.g., illustration or photograph) cannot be a type specimen (I believe the ICNafp accommodates "iconotypes"). Rather, the organism depicted in an image is regarded as being the type specimen. 2) A type specimen consists of the entire organism. For example, in the case of a mammal that is captured and separated into its fur, skeleton, alcoholic-preserved tissues, and tissue samples for DNA analysis, all of these things together constitute the type specimen. In other words, the whole specimen is the type. This is in contrast to ICNafp, where a single specimen from a tree (for example) is the type, whereas other specimens taken from the same tree are isotypes, and the remainder of the tree is not a type at all. 3) It is understood that the community of organisms inhabiting a type specimen (e.g., parasites and commensals) do not form part of the type specimen. There are other issues as well (especially for ichnotaxa, colonies, and other specific cases), but the general point is that under the ICZN Code, a type specimen consists of the sum of all cells that contain the same DNA material that were part of the same biological individual (i.e., identical twins, clones, and parthenogenic and other asexually reproducing organisms potentially contain the same DNA material, but are different "individuals"). Most of the above is pretty straight-forward. Where it gets a bit squishy is when you go down below the "tissue sample" level into smaller and smaller subunits. Can a single cell containing intact DNA be a type specimen for a multicellular organism? Can a single DNA molecule be a type specimen? Can a single chromosome be a type specimen? Can a PCR product be a type specimen? ...you can add as many hair-splitting examples as you wish. Conversations like this let me to draw a distinction between matter that is actually from an organism, vs. stuff that is representative of the organism but lacks any material connection to the organism. Coming back to Dan Janzen's comment; I would conclude that most things that would full under the term "materialSample" include actually matter from a biological organism. A PCR product is borderline, because it presumably does contain actual matter from the organism, but the vast majority of matter in the PCR product was not from the organism. Once you lose all the matter from the organism, you are no longer talking about the "individual", but instead are now talking about "Evidence of the Individual". This applies to images of the individual (whether taken in-situ, or in a lab), DNA "sequences" (rendered as text), images of the results of DNA sequencing analysis (in various forms), and various other non-biological derivatives. So, this leads me to the comment from Steve about "Evidence" (which, if I understand correctly, is conceptually the same as the DSW "Token": https://code.google.com/p/darwin-sw/wiki/ClassToken) In our model, a specimen is *not* a Token or Evidence -- it is an individual. This has proven (in my mind at least -- Rob W. still has reservations) to be a MUCH more practical way to think of, and manage data for, specimens. This email will be WAY too long if I try to explain all the subtleties of this, so I'll just leave it at that. But clearly there are some differences between our notion of "Evidence", and the DSW concept of "Token" -- although both seem to be intended to solve the same problem. Enough for now.... Aloha, Rich

1 0

Fwd: SANBI Post Doctoral Fellowships
by John Wieczorek 08 May '13

08 May '13

Forwarding relevant opportunity announcement from South Africa. ---------- Forwarded message ---------- From: Gloria Cupido <G.Cupido(a)sanbi.org.za> Date: Wed, May 8, 2013 at 5:17 AM Subject: SANBI Post Doctoral Fellowships To: Paula Hathorn <P.Hathorn(a)sanbi.org.za> Dear all **** ** ** Please see on the SANBI website adverts for the two biodiversity informatics post doctoral fellowships based at the University of the Western Cape http://www.sanbi.org/jobs/post-doctoral-fellowship-interrogation-biodiversi… http://www.sanbi.org/jobs/post-doctoral-fellowship**** ** ** Please circulate these adverts to potential candidates who will add value to the programme we are establishing.**** ** ** Kind regards**** ** ** Paula**** ** ** ** ** Paula Hathorn**** Learning Network Manager**** Biodiversity Information Management **** South African National Biodiversity Institute **** Tel: +27 21 799 8885**** Cell: +27 82 2608584**** Fax2email: 0865208130**** ** ** ------------------------------ Please visit our website www.sanbi.org for more information about the South African National Biodiversity Institute . Think before you print. Please consider the environment before printing this email. NOTE: This email and any attachments are intended for the addressee only, and contain information that may be legally privileged and / or confidential and / or the subject of copyright that is protected by law. Any unauthorised usage, disclosure, alteration or dissemination is prohibited. The SANBI accepts no responsibly for any loss whether it be direct, indirect or consequential, arising from information made available and actions resulting there from. No liability is accepted by the SANBI or the sender. The views or opinion expressed in this email message may not necessarily be that of the SANBI or the SANBI Management. The SANBI reserves the right to monitor all email communication. Please consider the environment before printing this email. The disclaimer is located at http://www.sanbi.org/node/5672

1 0

Completion of Audubon Core public review
by Steve Baskauf 25 Apr '13

25 Apr '13

More than the minimum 30 days required for the public review of Audubon Core have passed and I've received comments from everyone who told me that they planned to comment. I am therefore closing the public review period. The review guidelines at http://www.tdwg.org/fileadmin/documentation/guidance_docs/ReviewManagerGuid… require that Public Review comments be visible to all. Since many of the comments I received were emailed directly to me rather than to the tdwg-content list or posted on the Issues Tracker, I've posted a digest of the comments at http://code.google.com/p/auduboncore/wiki/RecordOfPublicReview for public inspection. As a result of these comments, a number of issues have been opened by commenters or by me based on the submitted comments. These issues can be viewed at the Audubon Core Issue Tracker http://code.google.com/p/auduboncore/issues/list I would like to thank everyone who took the time to read the specification and comment. I think that the standard will be strengthened based on your comments and look forward to working with the authors to implement many of your suggestions. Steve Baskauf Audubon Core Review Manager -- 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

New listserv: Domain Modelling in Flower-Visiting
by Willem Coetzer 23 Apr '13

23 Apr '13

Please visit https://lists.ru.ac.za/mailman/listinfo/dmfv to subscribe. Looking forward to continuing the discussion about the semantics of flower-visiting and flower-visitors. [cid:image54ec2c.PNG@77a2217a.4d8c34f3] Somerset Street Willem Coetzer Grahamstown, 6139 Biodiversity Information Manager Private Bag 1015 Tel: +27 46 603 5841 Grahamstown, 6140 Fax: +27 46 622 2403 South Africa Email: W.Coetzer(a)saiab.ac.za<mailto:W.Coetzer@saiab.ac.za> http://www.saiab.ac.za/<http://http://www.saiab.ac.za/> Disclaimer:<http://www.nrf.ac.za/email-legal-notice.php> http://www.nrf.ac.za/email-legal-notice.php Please consider the environment before printing this message.

1 0

What is the purpose of dcterms:accessRights in Darwin Core?
by Steve Baskauf 18 Apr '13

18 Apr '13

I have been struggling with some difficult terms while working on the draft Darwin Core RDF Guide. At the moment, the term that I've been struggling with is dcterms:accessRights, which is imported by Darwin Core from Dublin Core as a record-level term. In the case of dcterms:accessRights (defined as "Information about who can access the resource or an indication of its security status." with comment "Access Rights may include information regarding access or restrictions based on privacy, security, or other policies."), the range is given as dcterms:RightsStatement (i.e. a non-literal value is expected rather than a string literal). Thus a client interpreting a dcterms:accessRights property should expect a URI reference pointing to another resource that is a Rights Statement, defined as "A statement about the intellectual property rights (IPR) held in or over a Resource, a legal document giving official permission to do something with a resource, or a statement about access rights." So dcterms:accessRights seems to be a rather vague term that is intended to point to additional information about: 1. intellectual property rights (i.e. copyright) 2. permission to do something with a resource (i.e. licensing information) 3. access rights (i.e. to what extent access to the resource is controlled) These are actually three rather different types of information about a resource. It seems to me that the first two items are about created intellectual property - the territory of Audubon Core. Audubon Core has a pretty rich vocabulary for describing these kinds of properties that media are likely to have. But they don't seem to apply so much to Darwin Core, which is more about data and specimens, neither one of which can be copyrighted or licensed as far as I can know. So it seems to me that item 3 is the most relevant to Darwin Core, since data can be embargoed, access to specimens can be restricted, loans prohibited, etc. The ancient history on the accessRights term at http://dublincore.org/usage/meetings/2002/10/accessRights.shtml seems to indicate that the term was originally intended to serve to describe the limitations of access but that it got thrown together with intellectual property rights and licensing when the range was declared to be "RightsStatement" several years later. Anyway, I'm not how this term would get used in the context of specimens and observations. The DwC comment give the example "not-for-profit use only" which sounds more like a licensing statement such as Creative Commons-NC . When Audubon Core comes online, xmpRights:UsageTerms and xmpRights:WebStatement will be available to provide that kind of information for images and other media. We also have dwc:informationWithheld to tell people that some information is not available to the public. So under what circumstances would I actually use dcterms:accessRights? Is there anybody who uses it as a property in their metadata and can give me some real examples of its use? I'm sure there was a reason given when Darwin Core was undergoing ratification, but I don't remember the discussion, and it is too overwhelming to think of digging through the email archives to look for it. Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: PMB 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 322-4942 If you fax, please phone or email so that I will know to look for it. http://bioimages.vanderbilt.edu

1 0

Re: [tdwg-content] tdwg-content Digest, Vol 48, Issue 4
by Éamonn Ó Tuama [GBIF] 16 Apr '13

16 Apr '13

The best practice that we should encourage is that terms should not be defined adhoc when creating Darwin Core extensions, but rather come from a published vocabulary (ideally expressed in RDF). The vocabulary work at GBIF supported by the EU ViBRANT project recognized this and it is something we are taking forward in the TDWG vocabulary management task group [1]. Éamonn [1] http://community.gbif.org/pg/groups/21382/vocabulary-management/ Message: 2 Date: Mon, 15 Apr 2013 15:58:32 +0000 From: Chuck Miller <Chuck.Miller(a)mobot.org> Subject: Re: [tdwg-content] Darwin Core To: "<tuco(a)berkeley.edu>" <tuco(a)berkeley.edu> Cc: TDWG Content Mailing List <tdwg-content(a)lists.tdwg.org> Message-ID: <A378AC48-A491-4D38-9CD5-04AD8C941792(a)mobot.org> Content-Type: text/plain; charset="us-ascii" On this same subject, what about the various Darwin Core term extensions at GBIF that are used by the GBIF Darwin Core Archive Validator? http://tools.gbif.org/dwca-validator/extensions.do There are a number of terms being created outside NCD and Darwin Core and TDWG. What does this mean to the TDWG Ontology and TDWG Vocabularies in general? Do we need formal multi-term synonymy or cross referencing to embrace the emerging real world of multiple overlapping terms standards? Chuck On Apr 15, 2013, at 10:45 AM, "John Wieczorek" <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> wrote: Dear all, I have been asked to cross-post here from a comment on the GBIF Community site discussion of "The Management of TDWG Ontologies and Darwin Core" (http://community.gbif.org/pg/forum/topic/29426/discussion-of-management-of- the-tdwg-ontologies-and-darwin-core/). Given the subject matter, I feel like the whole discussion should take place in the broader audience reached by this list. While managing the Darwin Core, I advocated not to re-use any term that had no status as a standard. It was partially for this reason that geo:lat and geo:long were rejected (see http://code.google.com/p/darwincore/issues/detail?id=82) It worries me a little to see a non-standard term (ncd:taxonCoverage, adopted in turn from the TDWG Ontology, also not a standard, see http://rs.tdwg.org/ontology/voc/Collection#taxonCoverage) being proposed for adoption into the Audubon Core (see http://terms.gbif.org/wiki/Audubon_Core_Term_List_%281.0_normative%29#ncd:ta xonCoverage). Does that bother anyone else? The alternative, sadly, is to make up a new term for ratification with the new standard. So, questions. If Audubon Core is ratified with the Natural Collections Descriptions (NCD) term in it, does that one term from NCD become a standard term? Under what governance? What about the rest of the NCD namespace? What about the TDWG Ontology. A lot of work went into both of those, but each lost its champions and they remain incompletely reviewed, especially in the context of all that has come to pass since they were active. I know that people refer to the TDWG Ontology fairly often in discussions, and that activity is still fomenting around that work with the imminent publication of the RDF Guide for Darwin Core. But what about NCD. What should we do with it? Does more than one person, group, or project still want to use it? If not, there isn't a lot of reason to go to the trouble of creating a data sharing standard if no one will use it to share. But if its need is still alive and active, who can take up the standard and promote its completion, review, and ratificatio n? Cheers, John _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org<mailto:tdwg-content@lists.tdwg.org> http://lists.tdwg.org/mailman/listinfo/tdwg-content

1 0

(no subject)
by John Wieczorek 15 Apr '13

15 Apr '13

Dear all, I have been asked to cross-post here from a comment on the GBIF Community site discussion of "The Management of TDWG Ontologies and Darwin Core" ( http://community.gbif.org/pg/forum/topic/29426/discussion-of-management-of-…) Given the subject matter, I feel like the whole discussion should take place in the broader audience reached by this list. While managing the Darwin Core, I advocated not to re-use any term that had no status as a standard. It was partially for this reason that geo:lat and geo:long were rejected (see http://code.google.com/p/darwincore/issues/detail?id=82) It worries me a little to see a non-standard term (ncd:taxonCoverage, adopted in turn from the TDWG Ontology, also not a standard, see http://rs.tdwg.org/ontology/voc/Collection#taxonCoverage) being proposed for adoption into the Audubon Core (see http://terms.gbif.org/wiki/Audubon_Core_Term_List_%281.0_normative%29#ncd:t…) Does that bother anyone else? The alternative, sadly, is to make up a new term for ratification with the new standard. So, questions. If Audubon Core is ratified with the Natural Collections Descriptions (NCD) term in it, does that one term from NCD become a standard term? Under what governance? What about the rest of the NCD namespace? What about the TDWG Ontology. A lot of work went into both of those, but each lost its champions and they remain incompletely reviewed, especially in the context of all that has come to pass since they were active. I know that people refer to the TDWG Ontology fairly often in discussions, and that activity is still fomenting around that work with the imminent publication of the RDF Guide for Darwin Core. But what about NCD. What should we do with it? Does more than one person, group, or project still want to use it? If not, there isn't a lot of reason to go to the trouble of creating a data sharing standard if no one will use it to share. But if its need is still alive and active, who can take up the standard and promote its completion, review, and ratification? Cheers, John

2 1