- tdwg-content - lists.tdwg.org

Darwin Core and phylogenies
by Roderic Page 16 Apr '15

16 Apr '15

My apologies in advance if this has come up before. Historically it seems that phylogenetics and classical biodiversity informatics live in separate worlds, for a bunch of reasons. One area they clearly intersect though is “phylogeography” or “geophylogenies”. I’ve been playing simple ways to create and visualise geophylogenies (e.g., http://iphylo.blogspot.co.uk/2015/01/geojson-and-geophylogenies.html ) and it occurs to me that it might be useful to have a Darwin Core-style way of encoding these. Phylogenetic data is typically stored very differently from the simple row-based approach adopted by Darwin Core (e.g., NEXUS format, XML [yuck], or JSON [sometimes yucky if it’s full of XML-style baggage, but I digress]). This makes it a challenge to integrate phylogenetic data with projects such as GBIF. This lack of integration is regrettable, anyone looking at the rise of phylogeography and DNA barcoding will recognise that many classically-defined species are poor representations of actual biodiversity, even in taxa that we think we know quite well (e.g., vertebrates). Given that we can encode a phylogenetic tree as a set of rows, each one representing an edge in the tree (what those of a certain age would call and "ancestor function”), it would be easy to have a Darwin Core extension that had one row per node in the tree, optionally with branch lengths, and leaf nodes also labelled by occurrence id (the same id used in the standard occurrence table, where ideally most if not all would be georeferenced). In this way we could add geophylogenies to Darwin Core archives, and existing tools for importing these (e.g., GBIF) could simply ignore the phylogeny until such times as they can handle them, but other tools could read the trees and display them. Is anyone doing something along these lines? 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: Roderic.Page(a)glasgow.ac.uk<mailto:Roderic.Page@glasgow.ac.uk> Tel: +44 141 330 4778 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 ORCID: http://orcid.org/0000-0002-7101-9767 Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ ResearchGate https://www.researchgate.net/profile/Roderic_Page

1 0

Re: [tdwg-content] Problem when validating Simple Darwin Core Recordset file
by Mergen Patricia 15 Apr '15

15 Apr '15

Dear Martin Thanks for your mail. I forward your mail to the experts list who may advice further. With my best wishes Pat Le 5 Avr. 2015 08:20, "Seifert-Martin" <Seifert-Martin(a)t-online.de> a écrit : > Dear Madam or Sir, > > when validating a Simple Darwin Core Recordset file I get the following > error messages: > > File: http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd, line 100, column 71: > Cannot resolve the name 'dwc:sampleSizeValue' to a(n) 'element > declaration' component. > <xs:element ref="dwc:sampleSizeValue" minOccurs="0"/> > > File: http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd, line 101, column > 70: > Cannot resolve the name 'dwc:sampleSizeUnit' to a(n) 'element declaration' > component. > <xs:element ref="dwc:sampleSizeUnit" minOccurs="0"/> > > File: http://rs.tdwg.org/dwc/xsd/tdwg_dwcterms.xsd, line 206, column 67: > Cannot resolve the name 'dwc:sampleSizeValue' to a(n) 'element > declaration' component. > <xs:element ref="dwc:sampleSizeValue" minOccurs="0"/> > > File: http://rs.tdwg.org/dwc/xsd/tdwg_dwcterms.xsd, line 207, column 66: > Cannot resolve the name 'dwc:sampleSizeUnit' to a(n) 'element declaration' > component. > <xs:element ref="dwc:sampleSizeUnit" minOccurs="0"/> > > Please, would you forward this e-mail to one of your technicians. > > Kind regards, > Martin Seifert > >

4 3

Linked Data and the Charm of Weak Semantics
by Bob Morris 13 Apr '15

13 Apr '15

"Linked Data and the Charm of Weak Semantics " Special section in http://www.asis.org/Bulletin/Apr-15/Bulletin_AprMay2015.pdf Bob -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Filtered Push Project Harvard University Herbaria Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://wiki.filteredpush.org http://wiki.datakurator.net http://taxonconceptexplorer.org/ http://www.cs.umb.edu/~ram

1 0

Clarification about values for dwc:county
by Steve Baskauf 13 Apr '15

13 Apr '15

The definition of dwc:county is: "The full, unabbreviated name of the next smaller administrative region than stateProvince (county, shire, department, etc.) in which the Location occurs." What I'm wondering about is whether the "full" name includes the second part to the name as it's typically written in the U.S. and Canada. "Missoula" is given as an example. However, the full name of that county in Montana is actually "Missoula County". If there were consistency in second parts of county names, one could just assume that one adds " County" after the value given for dwc:county. However, there isn't consistency. In Louisiana, it's "Washington Parish". In Alaska, names usually end with "Borough" (e.g. "Denali Borough"), although sometimes they don't (e.g. "Dillingham Census Area"). Outside the U.S. and Canada, there may be no second part to the name, or it might be something completely different. I am having a problem with this when I try to display values of dwc:county on a web page. Currently I have some rules that involve examining the country and the value of dwc:stateProvince to decide what to append after the first part of the name. But they don't work for Alaska and if I just said "Dillingham, Alaska" that would really be wrong if I meant the Dillingham Census Area and not the city of Dillingham. It would be easier to display them if the second part of the name were included in the value. Is there a convention on this? I was assuming that it would be to omit the second part of the name, but since the definition says "full, unabbreviated name", I'm not sure. 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 http://vanderbilt.edu/trees

4 5

Re: [tdwg-content] FW: domesticated species identifier in GBIF?
by Ramona Walls 12 Apr '15

12 Apr '15

Dear Daniela: The Biological Collections Ontology (BCO) <https://github.com/tucotuco/bco> maps Darwin Core terms to an ontology. One of our goals for doing this is so that we can work out the semantics of new terms requests before they are submitted to Darwin Core, thereby, we hope, avoiding circular and often hard to follow discussions on the mailing list. The process we suggest is to explore the definitions and semantics of terms in BCO, and then, once there is some agreement, request them to DwC if appropriate. In many case, new terms may not be needed for Darwin Core, but instead we can provide a controlled vocabulary to serve as the values for existing Darwin Core properties. We have a recent request for origin and establishment terms ( https://github.com/tucotuco/bco/issues/30) which we have begun working on. I think that your request for domestication status fits very nicely with this, and we could include terms as part of the same discussion. Would you be willing to add your comments and suggested definitions to the issue? Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden > > Today's Topics: > > 1. Re: FW: domesticated species identifier in GBIF? (Mergen Patricia) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 10 Apr 2015 19:16:36 +0200 > From: Mergen Patricia <mergen.patricia(a)gmail.com> > Subject: Re: [tdwg-content] FW: domesticated species identifier in > GBIF? > To: Daniela Soleri <soleri(a)geog.ucsb.edu>, tdwg-content(a)lists.tdwg.org > Message-ID: > < > CAKpZQj35tnhHX6joXVMXcEqq2JNjiuGcGPqQp9x_N0QgX9V5Yw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Daniela > > I forward your question to the TDWG-content list where experts can further > answer your questions. > you can also become member of the list here : > http://lists.tdwg.org/mailman/listinfo > > all the best > > Patricia > > On Fri, Apr 10, 2015 at 6:30 PM, Daniela Soleri <soleri(a)geog.ucsb.edu> > wrote: > > > Dear Patricia Mergen, > > > > I have been referred to the TDWG by the GBIF secretariat. I am very > > interested in pursuing the inclusion of the categories "domesticate" and > > "domesticate wild relative" as identifiers on the GBIF platform, which I > > believe will have wide utility for a diversity of users. Can you please > > tell me who I should contact, and/or the process of proposing and > > justifying such inclusions? > > > > Thank you for your assistance. Best wishes, > > > > Daniela Soleri > > > > > > > > > > -------- Forwarded Message -------- Subject: FW: domesticated species > > identifier in GBIF? Date: Wed, 8 Apr 2015 10:20:59 +0200 From: GBIF > > Helpdesk <helpdesk(a)gbif.org> <helpdesk(a)gbif.org> To: > soleri(a)geog.ucsb.edu CC: > > Dmitry Schigel [GBIF] <dschigel(a)gbif.org> <dschigel(a)gbif.org>, 'GBIF > > Helpdesk' <helpdesk(a)gbif.org> <helpdesk(a)gbif.org>, portal(a)gbif.org > > > > Dear Daniela, > > > > We do not have an identifier for domesticated species and there is no > such property on the horizon either. GBIF is employing the Darwin Core > terms (http://rs.tdwg.org/dwc/terms/index.htm ) and you would need to > engage with TDWG if you want to submit recommendations. You can sign up for > the mailing list here:http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > If you have a list of the species of interest, I can generate a custom > download for you. > > > > > > Sincerely, > > > > Jan K. Legind > > GBIF Secretariat > > > > -----Original Message----- > > From: Daniela Soleri [mailto:soleri@geog.ucsb.edu <soleri(a)geog.ucsb.edu > >] > > Sent: Wednesday, March 25, 2015 6:20 PM > > To: info(a)gbif.org > > Subject: domesticated species identifier in GBIF? > > > > Is there a domesticated species identifier for GBIF entries so that it > is possible to search exclusively for or within domesticated species only? > Please let me know if any such identifier exists or is being planned. > > > > Thank you, > > > > -- > > Daniela Soleri, PhD > > Associate Research Scientist > > Geography Department > > UC Santa Barbara > > Santa Barbara, CA 93106-4060 > > > > > > > > > > > > > > > > > > >

1 0

Re: [tdwg-content] FW: domesticated species identifier in GBIF?
by Donald Hobern 11 Apr '15

11 Apr '15

Dear Daniela, I understand the value and interest of what you are seeking to achieve. However, it is a little more complicated. The Darwin Core data that you see in GBIF is from data shared by many different publishers from work on their collections or field research. Few of these data sets standardly mark all records e.g. as "alien" or "naturalised" or "domesticated" - because it is not necessarily a significant factor in the context of their research. For this reason, marking data which relates to "domesticated" organisms or "wild relatives" can only easily be handled as a secondary interpretation of the data. This would be possible if we had an agreed list of species which should be tagged this way. It may however be that the tags should only apply in certain localities, since the species may exist in the wild in other areas. This introduces more complexity. For this reason, right now, it makes most sense for researchers to identify the list of species of interest to them and the areas of interest and filter data accordingly. If you are able to identify a suitable and generally useful list of species that could be of value to others, we can explore ways to make it accessible and to use it to tag the species in question. Sorry if this is not a quick answer, but I hope it helps. Best wishes, Donald Hobern GBIF Executive Secretary > Date: Fri, 10 Apr 2015 19:16:36 +0200 > From: Mergen Patricia <mergen.patricia(a)gmail.com> > Subject: Re: [tdwg-content] FW: domesticated species identifier in > GBIF? > To: Daniela Soleri <soleri(a)geog.ucsb.edu>, tdwg-content(a)lists.tdwg.org > Message-ID: > < > CAKpZQj35tnhHX6joXVMXcEqq2JNjiuGcGPqQp9x_N0QgX9V5Yw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Daniela > > I forward your question to the TDWG-content list where experts can further > answer your questions. > you can also become member of the list here : > http://lists.tdwg.org/mailman/listinfo > > all the best > > Patricia > > On Fri, Apr 10, 2015 at 6:30 PM, Daniela Soleri <soleri(a)geog.ucsb.edu> > wrote: > > > Dear Patricia Mergen, > > > > I have been referred to the TDWG by the GBIF secretariat. I am very > > interested in pursuing the inclusion of the categories "domesticate" and > > "domesticate wild relative" as identifiers on the GBIF platform, which I > > believe will have wide utility for a diversity of users. Can you please > > tell me who I should contact, and/or the process of proposing and > > justifying such inclusions? > > > > Thank you for your assistance. Best wishes, > > > > Daniela Soleri > > > > > > > > > > -------- Forwarded Message -------- Subject: FW: domesticated species > > identifier in GBIF? Date: Wed, 8 Apr 2015 10:20:59 +0200 From: GBIF > > Helpdesk <helpdesk(a)gbif.org> <helpdesk(a)gbif.org> To: > soleri(a)geog.ucsb.edu CC: > > Dmitry Schigel [GBIF] <dschigel(a)gbif.org> <dschigel(a)gbif.org>, 'GBIF > > Helpdesk' <helpdesk(a)gbif.org> <helpdesk(a)gbif.org>, portal(a)gbif.org > > > > Dear Daniela, > > > > We do not have an identifier for domesticated species and there is no > such property on the horizon either. GBIF is employing the Darwin Core > terms (http://rs.tdwg.org/dwc/terms/index.htm ) and you would need to > engage with TDWG if you want to submit recommendations. You can sign up for > the mailing list here:http://lists.tdwg.org/mailman/listinfo/tdwg-content > > > > If you have a list of the species of interest, I can generate a custom > download for you. > > > > > > Sincerely, > > > > Jan K. Legind > > GBIF Secretariat > > > > -----Original Message----- > > From: Daniela Soleri [mailto:soleri@geog.ucsb.edu <soleri(a)geog.ucsb.edu > >] > > Sent: Wednesday, March 25, 2015 6:20 PM > > To: info(a)gbif.org > > Subject: domesticated species identifier in GBIF? > > > > Is there a domesticated species identifier for GBIF entries so that it > is possible to search exclusively for or within domesticated species only? > Please let me know if any such identifier exists or is being planned. > > > > Thank you, > > > > -- > > Daniela Soleri, PhD > > Associate Research Scientist > > Geography Department > > UC Santa Barbara > > Santa Barbara, CA 93106-4060 > > > > > > > > > > > > > > > > > > >

1 0

Re: [tdwg-content] FW: domesticated species identifier in GBIF?
by Mergen Patricia 10 Apr '15

10 Apr '15

Dear Daniela I forward your question to the TDWG-content list where experts can further answer your questions. you can also become member of the list here : http://lists.tdwg.org/mailman/listinfo all the best Patricia On Fri, Apr 10, 2015 at 6:30 PM, Daniela Soleri <soleri(a)geog.ucsb.edu> wrote: > Dear Patricia Mergen, > > I have been referred to the TDWG by the GBIF secretariat. I am very > interested in pursuing the inclusion of the categories "domesticate" and > "domesticate wild relative" as identifiers on the GBIF platform, which I > believe will have wide utility for a diversity of users. Can you please > tell me who I should contact, and/or the process of proposing and > justifying such inclusions? > > Thank you for your assistance. Best wishes, > > Daniela Soleri > > > > > -------- Forwarded Message -------- Subject: FW: domesticated species > identifier in GBIF? Date: Wed, 8 Apr 2015 10:20:59 +0200 From: GBIF > Helpdesk <helpdesk(a)gbif.org> <helpdesk(a)gbif.org> To: soleri(a)geog.ucsb.edu CC: > Dmitry Schigel [GBIF] <dschigel(a)gbif.org> <dschigel(a)gbif.org>, 'GBIF > Helpdesk' <helpdesk(a)gbif.org> <helpdesk(a)gbif.org>, portal(a)gbif.org > > Dear Daniela, > > We do not have an identifier for domesticated species and there is no such property on the horizon either. GBIF is employing the Darwin Core terms (http://rs.tdwg.org/dwc/terms/index.htm ) and you would need to engage with TDWG if you want to submit recommendations. You can sign up for the mailing list here:http://lists.tdwg.org/mailman/listinfo/tdwg-content > > If you have a list of the species of interest, I can generate a custom download for you. > > > Sincerely, > > Jan K. Legind > GBIF Secretariat > > -----Original Message----- > From: Daniela Soleri [mailto:soleri@geog.ucsb.edu <soleri(a)geog.ucsb.edu>] > Sent: Wednesday, March 25, 2015 6:20 PM > To: info(a)gbif.org > Subject: domesticated species identifier in GBIF? > > Is there a domesticated species identifier for GBIF entries so that it is possible to search exclusively for or within domesticated species only? Please let me know if any such identifier exists or is being planned. > > Thank you, > > -- > Daniela Soleri, PhD > Associate Research Scientist > Geography Department > UC Santa Barbara > Santa Barbara, CA 93106-4060 > > > > > > > > >

1 0

Notes on the Biological Collections Ontology
by Quentin Groom 27 Mar '15

27 Mar '15

Dear All, To acquaint myself with the Biological Collections Ontology I went through it and made some notes. John Wieczorek suggested I share these notes so that they can be responded to openly. They are as follows, I look forward to your comments. 1. Why are the dates clustered together in one branch, but day, month, year separate? 2. eventDate: regarding date ranges. Sometimes an event continues for a period such as a field trip, but often a date range is required because although the event took place in a certain time frame, the exact event date is not known. There should perhaps be a way of distinguishing between these two situations. 3. Vernacular name should be associated with a language and a geographic area where it is used? 4. verbatimSRS, footprintSRS and geodeticDatum are similar but not the same. They seem to overlap. The SRS has a clear definition epsg- registry.org, but geodeticDatum is a more general term. The definitions and usages could be stronger. 5. There is a need for local grid reference systems. Many countries have their own ways of writing grid references and verbatimLongitude and verbatimLatitude are not suitable for these. For example, the UK has grid references such as NZ28F, which mean something very specific in the country. It is a similar situation in Belgium and I imagine other countries. 6. georeferenceVerificationStatus & identificationVerificationStatus: It is not clear how these should be used. The names are similar, but the described usage is very different. I find it hard to imagine how they would be used in practice. 7. There are occasions within biogeographic databases where you want to indicate that an observation or collection is not trusted. I can’t see a place where a record can be verified as a whole. For example, if it is suspected that the label has been muddled up or the collector is suspected of fraud. With an observation there is no specimen to verify, but the record should be verifiable. 8. member, lithostratigraphicTerms, bed etc etc. I don’t know anything about geology, but these terms seem to overlap and could perhaps be thought of as synonymous. It would be valuable to find records where these terms are required to see how they are used in practice. 9. county & stateProvince: These are parochial terms. There are many nested subdivisions of countries and there is probably a better way to describe them. Perhaps there is already a hierarchical ontology to describe geographic areas. 10. Abundance estimates: There are several ways to describe estimates of abundance, such as DOMAIN, DAFOR, percent coverage, is there a way to accommodate these? 11. Controlled vocabularies: Many terms suggest using a controlled vocabulary, but most don’t have one. Is this an area we should work on? 12. Consider the importance of citation and providence the “according to” information seems rather weak. There should perhaps be a space for an identifier (ORCID). Also, biographic information such as date of birth, date of death, institutional association. These are useful for providence, but also for validation of records. 13. What is the difference between fieldNumber and recordNumber? 14. establishmentMeans: the description seems to conflate three concepts, the length a taxon has been established at a location (e.g. native); the way it got to the location (e.g. introduced) and the dispersive ability of the taxon (e.g. invasive). To my mind the latter is not required as it is an opinion about the taxon as a whole not the observation. The first two should be separated to make them useful. People need to distinguish between the native status of a species at a location and how it got to that location. Invasive species biologists are particularly interested in the vectors of introduction. 15. The health of an animal or plant can be noted on an observation and is useful for analysis. Is there some way of stating that the organism was dead when the specimen or observation was made? Regards Quentin -- Dr. Quentin Groom (Botany and Information Technology) Botanic Garden, Meise Domein van Bouchout B-1860 Meise Belgium ORCID: 0000-0002-0596-5376 Landline; +32 (0) 226 009 20 ext. 364 FAX: +32 (0) 226 009 45 E-mail: quentin.groom(a)br.fgov.be Skype name: qgroom Website: www.botanicgarden.be

2 2

Darwin Core terms sex and lifeStage with mixed content
by John Wieczorek 26 Mar '15

26 Mar '15

Dear all, There is a body of topics surrounding Darwin Core terms for which it is tempting to overload the content in an effort to provide richer data than the standard would seem to support. We have a pair of older open issues on this general topic in the Darwin Core issue tracker. https://github.com/tdwg/dwc/issues/35 https://github.com/tdwg/dwc/issues/36 You can see in the discussions on those issues that there is some consensus that the content of Darwin Core terms should remain consistent with the definitions and not mix concepts. I've had recent questions in particular about the fields 'sex' and 'individualCount'. Here is an example. How should one populate Darwin Core terms for a record of 2 males and 5 females in a single lot? I propose that part of this is easy - the individualCount should be 7. The definition of the sex term (without looking for clues in the Comments) might be seen as a little ambiguous, "The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary." Strictly speaking, there is no single sex that matches the biological individuals in this example lot Occurrence record, and so the sex fields should be left blank. There are a number of terms in Darwin Core whose definitions suggest that a list (formatted with ' | ' as a separator) be used to match multiple values. Though it might seem that sex could be one of these terms, it isn't currently. Again this argues for a single value for sex from a controlled vocabulary. The biggest problem is with the Comment on the sex term, which gives an example with different semantics from what the definition says - namely "8 males, 4 females". I pose that this is an error and must be corrected. Yet, all hope of retaining information in the Occurrence record is not lost. To capture the richness of the information in the multi-sex lot example, I would recommend the use of dynamicProperties. How should one populate Darwin Core terms for a record of 2 males and 5 females in a single lot? I would do this: sex = null individualCount = 7 dynamicProperties= { "count of males":2, "count of females":5 } Hope that makes sense. Since this topic has arisen from multiple independent sources, I would like to formally propose changes to the sex and lifeStage terms to remove the spurious examples. Today begins a minimum 30-day public commentary period to close on 5 March 2015 if no dissenting opinions are made in this public forum. Here is how the new terms would appear if the changes are accepted: Identifier: http://rs.tdwg.org/dwc/terms/sex Namespace: http://rs.tdwg.org/dwc/terms/ Label: Sex Definition: The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary. Comment: Examples: "female", "hermaphrodite", "male". For discussion see http://terms.tdwg.org/wiki/dwc:sex Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2008-11-19 Date Modified: 2015-02-05 Has Domain: Has Range: Version: sex-2015-02-05 Replaces: Sex-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.06: DataSets/DataSet/Units/Unit/Sex Identifier: http://rs.tdwg.org/dwc/terms/lifeStage Namespace: http://rs.tdwg.org/dwc/terms/ Label: Life Stage Definition: The age class or life stage of the biological individual(s) at the time the Occurrence was recorded. Recommended best practice is to use a controlled vocabulary. Comment: Examples: "egg", "eft", "juvenile", "adult". For discussion see http://terms.tdwg.org/wiki/dwc:lifeStage Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2008-11-19 Date Modified: 2015-02-05 Has Domain: Has Range: Version: lifeStage-2015-02-05 Replaces: LifeStage-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/Occurrence ABCD 2.06: DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalSexualStage or DataSets/DataSet/Units/Unit/MycologicalUnit/MycologicalLiveStages/MycologicalLiveStage (Note DwC spec uses ”MycologicalLifeStage” or DataSets/DataSet/Units/Unit/ZoologicalUnit/PhasesOrStages/PhaseOrStage Cheers, John

7 10

Re: [tdwg-content] Darwin Core Proposal - term content recommendations to comments
by Ramona Walls 24 Mar '15

24 Mar '15

IAO:example of usage is widely used with object properties. I don't know how often it is used with data properties, but I don't know is any reason it could not be. I will file an issue about the truncated definition of iao:example of usage. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Scientific Analyst, The iPlant Collaborative, University of Arizona Research Associate, Bio5 Institute, University of Arizona Laboratory Research Associate, New York Botanical Garden On Tue, Mar 24, 2015 at 4:00 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: Darwin Core Proposal - term content recommendations to > comments (?amonn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 Mar 2015 16:48:54 +0100 > From: ?amonn ? Tuama [GBIF] <eotuama(a)gbif.org> > Subject: Re: [tdwg-content] Darwin Core Proposal - term content > recommendations to comments > To: 'Markus D?ring' <mdoering(a)gbif.org>, "'John Wieczorek'" > <tuco(a)berkeley.edu> > Cc: 'TDWG Content Mailing List' <tdwg-content(a)lists.tdwg.org> > Message-ID: <014601d06580$ddaf3210$990d9630$@org> > Content-Type: text/plain; charset="iso-8859-1" > > I can see how minting an additional term "dwcattributes:example" has a > certain consistency given the namespace is already in use but, as a close > alternative, and following best practice of not reinventing terms (and thus > making it easier for 3rd parties trying to process the RDF directly), I > think ?skos:example? is also worth considering. I am not familiar with > "iao:example of usage" but checking the definition [1]: > > ?A phrase describing how a class name should be used. May also include > other > kinds of examples that facilitate immediate understanding of a class > semantics, such as widely known prototypical subclasses or instances of the > class. Although essential for high level terms, examples for low level > terms > (e.g., Affymetrix HU133 array) are not? (definition looks truncated) > > > > ? it refers to classes rather than properties. The majority of DwC terms > are > properties. So, can "iao:example of usage" be applied to them? > > > > ?amonn > > > > [1] <http://purl.obolibrary.org/obo/IAO_0000112> > http://purl.obolibrary.org/obo/IAO_0000112 > > > > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Markus D?ring > Sent: 20 March 2015 14:35 > To: John Wieczorek > Cc: TDWG Content Mailing List > Subject: Re: [tdwg-content] Darwin Core Proposal - term content > recommendations to comments > > > > Thanks John, > > > > mostly repeating what I said earlier I would prefer to coin the new example > term in the existing dwcattributes namespace. > > It feels more consistent, is very straight forward and as you say we can > always declare same as relations elsewhere if that is really useful to > anyone. > > I cannot see any immediate advantage of reusing either the skos or the iao > term over minting a new one in the single dwcattributes namespace that > helps > documenting our dwc terms. > > > > Markus > > > > > > On 20 Mar 2015, at 14:14, John Wieczorek <tuco(a)berkeley.edu> wrote: > > > > > > Dear all, > > > > I would like to summarize my understanding of the state of the proposal to > put term content recommendations in comments consistently, rather than in > the definitions where they can sometimes be found. There has been universal > support for this idea. > > > > A second part of the proposal was to take this opportunity to separate the > examples from the comments using a distinct property to do so in the rdf > definitions of the terms. There has also been universal support for this > idea. > > > > Discussion revolved around how to accomplish the second part of the > proposal. I originally proposed a new attribute "dwcattributes:example", > which would be included once for every distinct example of term usage - > with > potentially many per Darwin Core term. There was universal support for the > idea of enabling this capability, though there was mixed opinion about > using > an existing term instead of minting a new one in the dwcattributes > namespace. Specifically, "skos:example" and "iao:example of usage" were > discussed. Potential problems with "skos:example" were pointed out. Similar > concerns about "iao:example of usage" were addressed, leaving this option > still open for consideration. > > > > It is not entirely clear technically (to me, anyway) how the annotation > property "iao:example of usage" would be imported into the normative rdf > document. I'm unaware of an OWL to RDF import mechanism. That doesn't mean > much, because I am not an expert. If there is not, I suppose we would have > to define an rdf file ourselves for the iao term and import that into > dwcattributes or into the normative Darwin Core rdf file(s) directly. I > don't think this would be a rigorous solution, but it would demonstrate our > intent fairly well, especially if there were comments to that effect in the > rdf files. Some guidance here might help us make a final decision on this > topic. > > > > If there is no clear and rigorous solution to the rdf import problem from > IAO, then it may just be easier to coin "dwcattributes:example" as > originally proposed, at least for now, and worry about it's equivalence to > "iao:example of usage" on the ontology side (BCO). > > > > I would really like to get the broader issue resolved soon, as we do > already > have consensus on making the contents of the definitions and comments > consistent. If we can't resolve how to separate the examples (even though > we > agree that it is a good idea), I will propose that we forget that added > part > of the proposal and just deal with the consistency issue first. > > > > Comments encouraged, as always. > > > > Cheers, > > > > John > > > > On Thu, Feb 5, 2015 at 10:01 AM, Ramona Walls <rlwalls2008(a)gmail.com> > wrote: > > As far as I know, iao:example of usage also allows both literals and URLs > as > the range. However, I fail to see a serious problem with that, and to me, > the benefits of re-using existing properties far outway the benefits I > could > see from having a separate set of properties for literals. Also, I don't > know anyone who reasons over annotations properties, although I am sure > there are those who do. > > In response to Paul Morris's comment, simply using iao:example of usage > does > not import all of IAO, and therefore does not include any of the "baggage" > of using IAO. > > Ramona > > > > > ------------------------------------------------------ > Ramona L. Walls, Ph.D. > Scientific Analyst, The iPlant Collaborative, University of Arizona > Research Associate, Bio5 Institute, University of Arizona > Laboratory Research Associate, New York Botanical Garden > > > > On Thu, Feb 5, 2015 at 10:48 AM, Richard Pyle <deepreef(a)bishopmuseum.org> > wrote: > > Like others, I like the idea in principle, but I?m not well-versed in the > implications of alternate approaches to implementation to weigh in on that. > Whatever technical solution is adopted, I would like to hope that it > supports the representation of more than a single example; as sometimes it > is useful to show alternate forms of acceptable content. > > > > Aloha, > > Rich > > > > > > From: tdwg-content-bounces(a)lists.tdwg.org > [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of John Wieczorek > Sent: Thursday, February 05, 2015 7:22 AM > To: Paul J. Morris > Cc: TDWG Content Mailing List; Ramona Walls > Subject: Re: [tdwg-content] Darwin Core Proposal - term content > recommendations to comments > > > > Does anyone have similar concerns about iao:example? > > > > On Thu, Feb 5, 2015 at 2:09 PM, Paul J. Morris <mole(a)morris.net> wrote: > > On Thu, 5 Feb 2015 11:17:58 -0500 > Bob Morris <morris.bob(a)gmail.com> wrote: > > But skos:note and its subproperties (including skos:example) can take > > literals or references [1]. To me, that weighs more than the > > baggage of minting two new terms. > > Also, SKOS, unless care is taken to import the Owl-DL version, brings > you into Owl-Full, with undesirable consequences for those who wish to > do reasoning. In early versions of dwcFP, we did include SKOS terms, > but removed them because of the consequences for reasoning. > > SKOS has some nice terms, reuse is a nice idea, but it comes with > significant knowledge engineering consequences. > > -Paul > -- > Paul J. Morris > Biodiversity Informatics Manager > Harvard University Herbaria/Museum of Comparative Zo?logy > mole(a)morris.net AA3SD PGP public key available > > _______________________________________________ > 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 > > > >

1 0