November 2014 - tdwg-content

RFC 2119: Re: Public comment on the Darwin Core RDF Guide
by Paul J. Morris 14 Dec '14

14 Dec '14

Bob Morris noted that it may be appropriate for the DarwinCore RDF Guide to follow RFC 2119 (something for which at least the TDWG GUID applicability statement provides precedent). The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in RFC 2119. Internet Engineering Task Force (IETF). RFC 2119. Key words for use in RFCs to Indicate Requirement Levels. http://www.ietf.org/rfc/rfc2119.txt This RFC notes: "These words are often capitalized" and "Imperatives of the type defined in this memo must be used with care and sparingly. In particular, they MUST only be used where it is actually required for interoperation or to limit behavior which has potential for causing harm". There are 69 occurrences of "should" in the guide, many of these instances appear to have the intent of colloqual english and probably other words should be substituted in those cases. I've taken a stab here at a set of cases where it feels like it might be appropriate to use the RFC 2119 imperatives. A question is whether it is the role of the guide to use MUST/MUST NOT/REQURED anywhere (except where that is forced by inheritance from elsewhere)? A potential place for asserting MUST/MUST NOT is the distinction between dwc and dwciri namespaces. I've put more discussion under the headings 2.4.1.2 and 2.5 below. -Paul ---- 1.3.2.1 Persistent Identifiers s/the provider should take care to ensure/the provider SHOULD take care to ensure/ s/it must be converted to an IRI/it MUST be converted to an IRI/ ---- 1.3.2.2 HTTP IRIs as self-resolving GUIDs s/through RDF should plan to implement GUIDs/through RDF MUST plan to implement GUIDs/ For consistency with "Must" in the GUID applicability statement. ---- 1.4.1 Well-known vocabularies s/the provider should assign the term an IRI,/the provider SHOULD assign the term an IRI,/ ---- 1.4.3 Use of Darwin Core terms in RDF s/each value should be referenced/each value MUST be referenced/ By the nature of object references. ---- 1.4.4 Limitations of this guide s/Darwin Core property terms should be used as RDF predicates and specifies that Darwin Core class terms should be used in rdf:type/Darwin Core property terms SHOULD be used as RDF predicates and specifies that Darwin Core class terms SHOULD be used in rdf:type/ ---- 1.5.5 Implications for expressing Darwin Core string values as RDF s/in which RDF should be structured/in which RDF SHOULD be structured/ ---- Example 1: s/Predicates must be identified by IRIs/Predicates MUST be identified by IRIs/ ---- 2.2 Subject resources s/it must be referenced by an IRI/it MUST be referenced by an IRI/ ---- 2.2.2 Associating a string identifier with a subject resource s/dcterms:identifier should be used to/dcterms:identifier SHOULD be used to/ s/it is acceptable to present it as a string literal value for dcterms:identifier/it MAY be presented as a string literal value for dcterms:identifier/ ---- 2.3.1.1 rdf:type statement s/The class should be identified by an IRI reference/The class MUST be identified by an IRI reference/ ---- 2.3.1.3 Explicit vs. inferred type declarations s/data providers should exercise caution in using any such term in a non-standard way/data providers SHOULD NOT use any such term in a non-standard way/ s/the provider should type the resource/the provider MAY type the resource/ ?? Or ?? s/the provider should type the resource/the provider SHOULD type the resource/ ---- 2.3.1.4 Other predicates used to indicate type s/in an RDF description should be considered optional, while including rdf:type should be considered highly recommended/in an RDF description is OPTIONAL, while rdf:type SHOULD be included/ s/A dwciri: analogue (Section 2.5) of dwc:basisOfRecord should not be used/A dwciri: analogue (Section 2.5) of dwc:basisOfRecord MUST NOT be used/ ---- 2.3.1.5 Classes to be used for type declarations of resources described using Darwin Core s/that should also be used/that SHOULD also be used/ ---- Example 9: s/a provider should include an xml:lang/a provider SHOULD include an xml:lang/ ---- Example 10: I'm not sure about this one: /language tags should be interpreted by clients s/may initially choose to expose literals without datatype attributes, they should/MAY initially choose to expose literals without datatype attributes, they SHOULD/ ---- 2.4.1.2 Terms intended for use with literal objects I'll put a stake in the ground for discussion here: Is the guide sufficiently normative to assert MUST (other than where that property is inherited from elsewhere)? If so, then the distinction between dwc and dwciri is the place to make that assertion: s/that terms in the dwc: namespace should be restricted to use with literal objects/that terms in the dwc: namespace MUST be restricted to use with literal objects/ ---- 2.4.2.1.1 Objects identified by LSIDs This one needs to be checked for consistency with the LSID Applicability Statements: s/version of the LSID should be used instead/version of the LSID SHOULD be used instead/ ---- Example 17: s/particular terms should be used with literal objects, or with IRI reference objects/particular terms SHOULD be used with literal objects, or SHOULD be used with IRI reference objects/ ---- 2.4.3.2 Literal values for non-literal resources in Darwin Core s/existing Darwin Core term in the dwc: namespace should have the same structure/existing Darwin Core term in the dwc: namespace SHOULD have the same structure/ ---- 2.5 Terms in the dwciri: namespace This is the companion case to 2.4.1.2 - is the distinction between dwciri and dwc to be asserted as SHOULD or MUST - using them incorrectly does have the "potential for causing harm" in the language of RFC 2119, but does the guide rise to the level of specifying an "absolute requirement of the specification". s/IRI reference objects and should NOT be used with literal/ IRI reference objects and MUST NOT be used with literal/ ---- 2.5.1 Definition of dwciri: terms s/resource described by a dwciri: property should be the subject of a triple for each value on the list/resource described by a dwciri: property SHOULD be the subject of a triple for each value on the list/ A counter example here comes from the Harvard List of Botanists, where http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/305dcac3-a748-4f47-8a18-… references the collector team "J. D. Hooker & A. Gray", that is, http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/cc3b7080-5fbb-4ea5-9655-… and http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/3f8c70aa-1862-4784-8a53-… ---- 2.5.3 Expectation of clients encountering RDF containing dwc: and dwciri: terms Instances of "should" here again cut to the heart of how strong the guidance is concerning dwc and dwciri. ---- Table 3 s/they should be used rather than using the Darwin Core ID/they SHOULD be used rather than using the Darwin Core ID/ ---- Example 22: s/The following points about the Example 22 should be noted:/Note the following points about Example 22:/ s/related non-literal resources should use/related non-literal resources SHOULD use/ /LSIDs are the objects of triples, they should be As with 2.4.2.1.1, this guidance needs to be checked against the GUID and LSID applicability statements. I think I'm reading the GUID applicability statement as s/should/MUST/ here. ---- 2.7.1 What purpose do convenience terms serve? s/In general, it should not be necessary for a data provider/In general, a data provider does not need/ ---- 2.7.3 Ownership of a collection item s/of the collection item should be indicated/of the collection item SHOULD be indicated/ ---- 2.7.4 Description of a taxonomic entity s/It is considered to be out of the scope of this document to specify how taxon concepts should be rendered as RDF/It is out of the scope of this document to specify how to render taxon concepts as RDF/ s/terms for taxonomic entities should be properties of dwc:Identification/terms for taxonomic entities MAY be properties of dwc:Identification/ s/The task of describing taxonomic entities using RDF must be an effort outside of Darwin Core/The task of describing taxonomic entities using RDF is out of scope of this document/ ---- 2.8.3 Expressing Darwin Core association terms as RDF with URI references s/it should be used to declare the type/rdf:type SHOULD be used to declare the type/ ---- Tables 3.4 to 3.7. s/should/SHOULD/ -------- -- Paul J. Morris Biodiversity Informatics Manager Harvard University Herbaria/Museum of Comparative Zoölogy mole(a)morris.net AA3SD PGP public key available

5 16

terms for sample data in DwC
by Éamonn Ó Tuama [GBIF] 12 Dec '14

12 Dec '14

In compliance with the directions for requesting changes to the Darwin Core (DwC) vocabulary, we hereby submit to the TDWG Content list a proposal for five new terms to express information on sample-based data. Sample-based data is a type of data available from thousands of environmental, ecological, and natural resource investigations. These can be one-off studies or monitoring programmes. Such data are usually quantitative, calibrated, and follow certain protocols so that changes and trends of populations can be detected. This is in contrast to opportunistic observation and collection data which today form a significant proportion of openly accessible biodiversity data. Sample-based data are often not shared because the underlying protocols have been hard to encode in a standardised way. For further background information and examples, please consult the sample data primer document [1]. We cannot emphasise enough that our intention here is not to establish how data should be captured or modelled but rather demonstrate one way data can be exposed to maximize discoverability and reuse. In particular, GBIF, in association with EU BON [2] project partners, is exploring how the IPT and Darwin Core Archives can enable the flow of sample based data in support of GEO BON Essential Biodiversity Variables (EBVs) [3]. While DwC already provides many terms that are relevant for describing sample-based data, based on several inputs (GBIF organised workshop on sample data, May 2013 ; previous discussions on the TDWG mailing list; discussions on the EU BON mailing list), we have identified a need for five new terms. These are: sampleSize <https://github.com/tdwg/dwc/issues/10> https://github.com/tdwg/dwc/issues/10 #Justification Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition A numeric value for the time duration, length, area or volume involved in the sampling event. #Comment The terms sampleSize and sampleSizeUnit are required to be used as a pair. The value of sampleSize is a number. Example: 5 for the value part of 5m. #Term group Event sampleSizeUnit <https://github.com/tdwg/dwc/issues/11> https://github.com/tdwg/dwc/issues/11 #Justification Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition The unit of measurement used in the sampling event. #Comment The terms sampleSize and sampleSizeUnit are required to be used as a pair, e.g., 5 metre. Example values of sampleSizeUnit include minute, hour, day, metre, square metre, cubic metre. Recommended best practice is to use a controlled vocabulary such as the Ontology of Units of Measure <http://www.wurvoc.org/vocabularies/om-1.8/> http://www.wurvoc.org/vocabularies/om-1.8/ of SI units, derived units or other non-SI units accepted for use within the SI (e.g. minute, hour, day, litre). Example: metre for the unit part of 5m. #Term group Event quantity <https://github.com/tdwg/dwc/issues/12> https://github.com/tdwg/dwc/issues/12 #Justification Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e. sampling events). For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition The quantity, per sampling event, given as a number or enumeration value for the quantityType. #Comment The terms quantity and quantityType are required to be used as a pair. The value of quantity is a number or enumeration. Examples: 12.5, r #Term group Occurrence quantityType <https://github.com/tdwg/dwc/issues/13> https://github.com/tdwg/dwc/issues/13 #Justification Required for sharing organism abundance data from controlled sampling and monitoring surveys (i.e., sampling events). For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition The entity to which the number or enumeration reported in quantity refers. #Comment The terms quantity and quantityType are required to be used as a pair, e.g., 14 individuals. The value of quantityType (i.e., the entity being measured) is expected to be drawn from a small controlled vocabulary. Examples: Individuals, % Biomass, % Biovolume, % species, % coverage, BraunBlanquetScale, DominScale. #Term group Occurrence parentEventID <https://github.com/tdwg/dwc/issues/9> https://github.com/tdwg/dwc/issues/9 #Justification Allows arbitrary linking of sub sampling events, e.g., for nested sampling plots. This was demanded by several people during the discussion of the TDWG sample based data session. For an introduction to the sampling proposal please see <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer. #Definition An event identifier for the super event which is composed of one or more sub-sampling events. #Comment The value must refer to an existing eventID. If the identifier is local it must exist within the given dataset. Example: A1 identifying the main Whittaker Plot in nested samples, each with their own eventID (e.g., A1:1, A1:2). #Term group Event None of the existing DwC terms is sufficient for any of the proposed terms although two are somewhat related: sampleEffort ("The amount of effort expended during an Event") and individualCount ("The number of individuals represented present at the time of the Occurrence"). Neither are adequate sampleEffort just provides a free text statement so is hard to parse in comparison to sampleSize and sampleSizeUnit and individualCount refers exclusively to individuals and not percentages or entities like biomass, biovolume, etc. [1] <http://links.gbif.org/ipt-sample-data-primer> http://links.gbif.org/ipt-sample-data-primer [2] <http://eubon.eu/> http://eubon.eu [3] <http://www.earthobservations.org/documents/cop/bi_geobon/ebvs/201301_ebv_pa per_pereira_et_al.pdf> http://www.earthobservations.org/documents/cop/bi_geobon/ebvs/201301_ebv_pap er_pereira_et_al.pdf ____________________________________________________ Éamonn Ó Tuama, Markus Döring, GBIF Secretariat

3 4

Re: [tdwg-content] RFC 2119: Re: Public comment on the Darwin Core RDF Guide
by Paul J. Morris 29 Nov '14

29 Nov '14

On Sat, 29 Nov 2014 17:08:36 -0500 Jonathan A Rees <rees(a)mumble.net> wrote: > Do you know of any precedent for 2119 language to be used in a > vocabulary specification? I'd be very interested to see that... http://www.w3.org/Submission/sioc-related/ http://rdfs.org/resume-rdf/ http://www.openarchives.org/ore/1.0/vocabulary https://dvcs.w3.org/hg/gld/raw-file/default/people/index.html http://www.openannotation.org/spec/alpha2/ http://socsem.open.ac.uk/ontologies/curio/ http://www.w3.org/community/odrl/two/vocab/ http://www.w3.org/TR/HTTP-in-RDF10/ http://www.w3.org/TR/vocab-people/ http://www.w3.org/TR/vocab-data-cube/ http://www.w3.org/TR/EARL10-Guide/ -Paul -- Paul J. Morris Biodiversity Informatics Manager Harvard University Herbaria/Museum of Comparative Zoölogy mole(a)morris.net AA3SD PGP public key available

1 0

Public comment on the Darwin Core RDF Guide
by Steve Baskauf 26 Nov '14

26 Nov '14

The Darwin Core standard contains several non-normative documents that describe how Darwin Core terms can be used in various contexts such as simple text [1] and XML [2]. Members of the RDF/OWL Task Group [3] have authored a guide describing how Darwin Core terms can be used in RDF. This guide has been subjected to extensive review by the Task Group and has been recommended by the Task Group as an addition to the Darwin Core standard under the Darwin Core Namespace Policy [4]. If ratified, the guide will be another non-normative document that is part of the standard, and a parallel guide to the existing text and RDF guides. The purpose of this email is to initiate the required 30 day public comment period before the proposed addition advances to the Executive Committee for ratification. Before commenting on the proposal, please begin by reading the cover page at https://code.google.com/p/tdwg-rdf/wiki/DwcRdf . The cover page includes the rationale for the guide, links to the proposed guide itself, supporting ancillary documents, and a history of the development of the guide. To comment, post to the tdwg-content email list (tdwg-content(a)lists.tdwg.org). Please use a descriptive subject line that differentiates your comment from other comments that deal with different aspects of the proposal. Comments will be tracked on the RDF/OWL Task Group's issue tracker [5]. The comment period will continue through at least 2014-12-26, but may be extended if discussion is ongoing. Steve Baskauf TDWG RDF/OWL Task Group co-convener [1] http://rs.tdwg.org/dwc/terms/guides/text/index.htm [2] http://rs.tdwg.org/dwc/terms/guides/xml/index.htm [3] https://code.google.com/p/tdwg-rdf/ [4] http://rs.tdwg.org/dwc/terms/namespace/index.htm [5] https://code.google.com/p/tdwg-rdf/issues/list -- 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

1 0

NIH Request for Information on Making Big Data Usable
by Ramona Walls 19 Nov '14

19 Nov '14

Hi everyone, The NIH currently has an RFI on making big data usable: http://grants.nih.gov/grants/guide/notice-files/NOT-ES-15-002.html. "The NIH is interested in exploring how the BD2K initiative can contribute to the improvement of policies, governance, administrative procedures, and funding to support community-based standards (CBS) efforts to develop and/or extend data and/or metadata standards, and how these activities relate to other ongoing or nascent biomedical research activities. Within this context, ‘community’ encompasses a broad range of stakeholders who may be engaged in the process of data standards development and use, including technical developers, librarians, science domain experts, researchers, information scientists, vendors, funders, publishers, and other end users. - See more at: http://grants.nih.gov/grants/guide/notice-files/NOT-ES-15-002.html#sthash.S… " I know most of us do NSF, not NIH funded research, but I think that the work we do on biodiversity informatics has a lot of relevance to NIH research (particularly documentation of microbial biodiversity), and the lessons learned about community by TDWG are worth sharing and promoting. I was planning to draft a response from the point of view of the biodiversity ontology development, but we could also make it a larger biodiversity informatics response, and include all of TDWG. Alternatively, there could be one response from TDWG and one from the BCO/PCO groups, if someone is interested in taking the lead on a TDWG response. 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

1 0

New Darwin Core Release
by John Wieczorek 10 Nov '14

10 Nov '14

Dear all, Congratulations to our community for advancing the Darwin Core standard! The TDWG Executive Committee recently ratified various changes [1] to the Darwin Core, resulting in a new release that incorporates consensus in public commentary on proposed ideas, some of which have been under discussions for several years. The highlights of the changes are as follow: 1) A new class Organism [2] has been added, with associated terms and with a rearrangement of some terms from the Occurrence class. This change also resulted in the depracation of the individualID term in favor of the new organismID term. 2) The terms in the Darwin Core type vocabulary have been removed in favor of equivalent terms in the normal Darwin Core namespace. For those of you who care about namespaces, this is much cleaner than what we had before. For those of you who don't care about namespaces, you still benefit from cleaned up definitions of the Darwin Core classes, as well as not having to look on an obscure page to find out what a MachineObservation [3] is, for example. 3) Best practice recommendations have been added for how to populate the content of Darwin Core terms that support lists, such as higherClassification [4] and higherGeography [5]. The format of the content of the dynamicProperties [6] term is now recommended to be JSON on a single line. 4) The Dublin Core term "license" [7] is now recommended for use in Darwin Core in place of the "rights" term. In cases where a legal document proferring rights, such as the CC0 Public Domain Dedication [8], can be cited, license is the term in which that information should be captured, while the agent granting those rights would go in the rightsHolder term and any non-legally binding documentation about the expected behavior with respect to the information (community norms, for example - see those for Canadensys [9] and VertNet [10]) would go in the accessRights term. All of the documentation within the standard has been updated. Maintainers of tools and further documentation (including translations) should be aware of these changes and make updates accordingly. In an effort to facilitate more open maintenance of Darwin Core, the standard will be maintained on Github [11], while related documentation for the the terms and their translations will be maintained on the GBIF Semantic Media/Wiki [12], and further documentation will be moved from the Google Code development site [13] to a Darwin Core documentation repository in Github [14]. Issues related to the Darwin Core standard, including requests for clarification, changes, or additions, should be entered in the Github issue tracker for the Darwin Core Standard [15]. If you have any doubt about where to find Darwin Core documentation or tools, refer to the References section [16] of the Darwin Core Introduction. Now that the new release has been published, the Darwin Core Task Group, charged with the maintenance of the standard, will turn toward the following activities: 1) Complete the move to Github. 2) Generate more documentation with numerous examples of how to construct Simple Darwin Core for various types of data records. 3) Facilitate updates to profiles and software affected by these changes such as the Occurrence Core extension [17], the Darwin Core Archive Reader[18], and the Darwin Core API[19] ) 4) Facilitate the updates to the Darwin Core RDF Guide and integrate it into the body of the standard. 5) Facilitate the processing of new and outstanding proposals for changes to the Darwin Core. Broad topics currently include additions or changes for terms related to the classes Taxon (ranks and a ScientifName class), Event (sampling), MaterialSample (preparations and sequences), and Occurrence (environment). 6) Work with the Executive Committee to define the TDWG Standards maintenance process. 7) Update the archived release on the TDWG site as soon as the site reorganization is done. I hope this all comes as good news and that the efforts to accommodate the changes are painless, swift, and worthwhile. Cheers, John [1] http://rs.tdwg.org/dwc/terms/history/decisions/#Decision-2014-10-26_14 [2] http://rs.tdwg.org/dwc/terms/index.htm#organismindex [3] http://rs.tdwg.org/dwc/terms/index.htm#machineobservationindex [4] http://rs.tdwg.org/dwc/terms/index.htm#higherClassification [5] http://rs.tdwg.org/dwc/terms/index.htm#higherGeography [6] http://rs.tdwg.org/dwc/terms/index.htm#dynamicProperties [7] http://rs.tdwg.org/dwc/terms/index.htm#dcterms:license [8] http://creativecommons.org/publicdomain/zero/1.0/legalcode [9] http://www.canadensys.net/about/norms [10] http://www.vertnet.org/resources/norms.html [11] https://github.com/tdwg/dwc [12] http://kos.gbif.org/wiki/DarwinCore [13] https://code.google.com/p/darwincore/ [14] https://github.com/tdwg/dwc-documentation [15] https://github.com/tdwg/dwc/issues [16] http://rs.tdwg.org/dwc/index.htm#references [17] http://tools.gbif.org/dwca-validator/extension.do?id=http://rs.tdwg.org/dwc… [18] https://github.com/gbif/dwca-reader [19] https://github.com/gbif/dwc-api

1 0

Floristic regions of the world
by Markus Döring 06 Nov '14

06 Nov '14

Hello, TDWG lists as one of its prior standard the "Floristic regions of the world”: http://www.tdwg.org/standards/104/ Unfortunately we do not give any information about it at all. It seems to me that the work of Takhtajan, A. 1986 is the actual endorsed standard. Can someone verfiy this? Takhtajan, A. 1986. Floristic regions of the world, pp. vii-xiii. University of California Press http://www.isbnsearch.org/isbn/0520040279 http://en.wikipedia.org/wiki/Phytochorion#Takhtajan.27s_floristic_regionali… Thanks, Markus

5 5

Knowledge Representation in Systematic Biology - Edited book proposal
by Nico Franz 04 Nov '14

04 Nov '14

Looking for comments, ideas, potential contributors. Cheers, Nico http://taxonbytes.org/knowledge-representation-systematic-biology-edited-bo… *Nico M. Franz, Ph.D.* Associate Professor & Curator of Insects School of Life Sciences PO Box 874501 Arizona State University Tempe, AZ 85287-4501 Lab: (480) 965-2850 Collection:(480) 965-2036 Fax: (480) 965-6899 E-mail: nico.franz(a)asu.edu Website: http://taxonbytes.org Twitter: https://twitter.com/taxonbytes ASUHIC: http://symbiota4.acis.ufl.edu/scan/portal/collections/misc/collprofiles.php… WoNA: http://symbiota4.acis.ufl.edu/scan/portal/checklists/checklist.php?cl=1

1 0