July 2011 - tdwg-content - lists.tdwg.org

date elements in Darwin Core XML schemas
by John Wieczorek 24 Jul '11

24 Jul '11

Geoffrey Allen has asked for a clarification about the date fields in Darwin Core. Commentary about the problem is recorded in Issue 118 (http://code.google.com/p/darwincore/issues/detail?id=118) in the Darwin Core Issue Tracker. Below is an excerpt of my explanation. The bottom line for this mailing list is that I believe Geoffrey has revealed an error in the XML Schema http://darwincore.googlecode.com/svn/trunk/xsd/tdwg_dwcterms.xsd that should be amended. I'm posting it here for commentary to see if there is/was any good reason for restricting the dateTime elements in Darwin Core more than in the recommendation in the definition of the terms. If not, this is a proposal to change the types in that schema from xs:dateTime to dateTimeISO. Commentary from Issue 118 follows: Through the date terms (eventDate, dateIdentified, relationshipEstablishedDate, measurementDeterminedDate, dcterms:modified) in the Darwin Core recommend the ISO 8601 standard for dates, the XML application schema published at http://darwincore.googlecode.com/svn/trunk/xsd/tdwg_dwcterms.xsd implements the more restrictive xs:dateTime type for these terms. For example, <xs:element name="eventDate" type="xs:dateTime" substitutionGroup="dwc:anyEventTerm"/> I'm not sure what the rationale was for implementing these terms as xs:dateTime rather than the less restrictive type dateTimeISO (see below) defined in http://darwincore.googlecode.com/svn/trunk/xsd/tdwg_basetypes.xsd, especially since http://darwincore.googlecode.com/svn/trunk/xsd/tdwg_dwcterms.xsd imports that bastypes schema and has a comment specifically about the use of dateTimeISO, which it doesn't actually use. I believe this is an unintentional error in tdge_dwcterms.xsd, but will post this to the tdwg_content list to see if there is any dissenting opinion about "correcting" it. <xs:simpleType name="dateTimeISO"> <xs:annotation> <xs:documentation xml:lang="en"> The date and time expressed in a way conforming to a subset of ISO 8601. Meant to be exactly the same as DateTimeISO defined in ABCD. </xs:documentation> </xs:annotation> <xs:restriction base="xs:string"> <xs:pattern value="\d\d\d\d(\-(0[1-9]|1[012])(\-((0[1-9])|1\d|2\d|3[01])(T(0\d|1\d|2[0-3])(:[0-5]\d){0,2})?)?)?|\-\-(0[1-9]|1[012])(\-(0[1-9]|1\d|2\d|3[01]))?|\-\-\-(0[1-9]|1\d|2\d|3[01])"></xs:pattern> </xs:restriction> </xs:simpleType>

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New term resolution: identificationVerificationStatus
by John Wieczorek 23 Jul '11

23 Jul '11

Darwin Core Issues 105: http://goo.gl/A5lgy This is the most recent request for an addition to the Darwin Core. This term has nit yet undergone a public commentary. Though this term did not exist in any earlier version of the Darwin Core, there are precedents for it in HISPID, ITF2, and ABCD. Open Issues: Determine if there demand for this term from more than one "independent" source. Determine if there is any objection to adding this term to the Darwin Core.

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FW: Darwin Core vernacularName field
by Amanda Neill 21 Jul '11

21 Jul '11

I've often thought that when we talk about common/vernacular names we are speaking at two different levels of application. Many (most?) herbarium specimen labels do not include any vernacular name. Those object records would therefore have nothing in the vernacularName element, and would not be found in a database by searching with a vernacular name. However, one can also (perhaps more appropriately) apply vernacular name at the level of taxon, and well-designed interfaces might display this for ALL specimen objects belonging to that taxon, also allowing all specimens to be located and retrieved when a user searches by vernacular name only. But we must be able to represent BOTH vernacularName from the object label AND vernacularName as commonly applied to the taxon (because these might differ regionally). Can the DwC element do both? I too feel it is useful to indicate the language of the vernacular name and concatenate multiple vernacular names. One way we have done it is parenthetically: "Chives (English); Ciboulette (French)" but that may not be the right way to do it. Amanda Amanda K. Neill | Director of the Herbarium (BRIT-SMU-VDB) | BRIT <http://www.brit.org/> | 817.546.1842 | 817.332.4112 fax | BRIT.org <http://www.brit.org/> | 1700 University Dr., Fort Worth, TX 76107-3400 USA | Think Before You Print ________________________________ From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Geoffrey Allen Sent: Thursday, July 21, 2011 10:24 AM To: tdwg-content(a)lists.tdwg.org Subject: [tdwg-content] Darwin Core vernacularName field Greeting, I have recently begun the process of digitising the 60,000 specimen vouchers from the UNB herbarium. The textual data for 40,000+ of those has already been entered into a database, and I am now trying to map those values to DwC so that we may share the data with other collections. I have some concern over the fact that simple DwC does not allow the repetition or extension of certain fields. The vernacularName field is a particular problem. New Brunswick is Canada's only officially bilingual province, as such, our specimens are all identified with both their English and French common names in the database. It would be very useful if we could extend DwC, creating something along the lines of <vernacularName lang=en>, or allow nesting of elements, perhaps in the form: <vernacularName> <English>Chives</English> <French>Ciboulette, brulotte</French> </vernacularName> The other option, as I see it, is that we store the English and French common names in our own fields, and then concatenate the two to create the DwC:vernacularName field. I see this option as less than ideal since it may hinder search/browsability. It may also cause a host of other problems from interpreting to storing the data. The herbarium with whom we first intent to share the data has already expressed a concern that their system cannot handle the diacritics found in many of the French names (!). They would like the Eng. common names, but not the French. This is more difficult to achieve if we concat the values. One additional thought is that the herbarium's imprint, _Flora of New Brunswick_, also includes common names in Maliseet and Mi'kmaq wherever possible. Although these two aboriginal languages do not currently exist in the dataset we are using, there is the potential that they may be added at some point in the future. It seems to me that the repetition of fields may be necessary in other instances too. I am having some difficulty figuring out how to record all the location data we have for the specimens, which are indicated using verbal descriptions, Lat/Long, UTM, and NTS coordinates - in many cases using all 4 for a single sample, but I will save the details for another posting. I will watch for the group's thoughts on this problem. Many thanks, Geoffrey -------------------------------------------- Geoffrey Allen Digital Projects Librarian Electronic Text Centre Harriet Irving Library University of New Brunswick Fredericton, NB E3B 5H5 Tel: (506) 447-3250 Fax: (506) 453-4595 gsallen(a)unb.ca _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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New terms need resolution: "Individual"
by John Wieczorek 20 Jul '11

20 Jul '11

Darwin Core Issues 69 and 80: http://code.google.com/p/darwincore/issues/list This issue is related to the issue of Evidence (CollectionObject, Representation, Token, Unit) covered in a previous posting. In the Darwin Core there is currently no separate class to explicitly represent the biological entities involved in an Occurrence. This is problematic when trying to be explicit about the attributes of these entities in the semantic world. Various names have been given to this concept, including "Individual", "BiologicalIndividual", "BiologicalEntity", "Organism", and "DataSets/DataSet/Units/Unit" in ABCD. Open Issues: Determine if there is a general consensus on the need for new class for this concept. The best name for this class. Create a new Type Vocabulary term referring to this new class. Decide which properties currently organized under Occurrence should instead be organized under this new class. As a seed for further discussion, here is a complete proposal. ============== Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/terms/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/terms/ Label: BiologicalEntity Definition: The category of information pertaining to an individual organism or a group of organisms that can reliably be known to represent a single taxon. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: {DataSets/DataSet/Units/Unit/CultureCollectionUnit or DataSets/DataSet/Units/Unit/MycologicalUnit or DataSets/DataSet/Units/Unit/HerbariumUnit or DataSets/DataSet/Units/Unit/BotanicalGardenUnit or DataSets/DataSet/Units/Unit/PlantGeneticResourceUnit or DataSets/DataSet/Units/Unit/ZoologicalUnit or DataSets/DataSet/Units/Unit/PalaeontologicalUnit or DataSets/DataSet/Units/Unit/MultimediaObjects/MultimediaObject} Term Name: BiologicalEntity Identifier: http://rs.tdwg.org/dwc/dwctype/BiologicalEntity Namespace: http://rs.tdwg.org/dwc/dwctype/ Label: BiologicalEntity Definition: A resource describing an instance of the BiologicalEntity class. Comment: For discussion see http://code.google.com/p/darwincore/wiki/DwCTypeVocabulary Type of Term: http://www.w3.org/2000/01/rdf-schema#Class Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Member Of: http://rs.tdwg.org/dwc/terms/DwCType Has Domain: Has Range: Version: BiologicalEntity-2011-07-04 Replaces: Is Replaced By: Class: ABCD 2.06: not in ABCD Term Name: biologicalEntityID Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityID Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityID Definition: An identifier for the set of information associated with an BiologicalEntity. May be a global unique identifier or an identifier specific to the data set. Comment: For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: http://purl.org/dc/terms/identifier Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: biologicalEntityID-2011-07-04 Replaces: individualID-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/ Term Name: biologicalEntityRemarks Identifier: http://rs.tdwg.org/dwc/terms/biologicalEntityRemarks Namespace: http://rs.tdwg.org/dwc/terms/ Label: biologicalEntityRemarks Definition: Comments or notes about the BiologicalEntity. Comment: Example: "seen several times in Tilden Park before capture". For discussion see http://code.google.com/p/darwincore/wiki/CollectionObject Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2009-07-04 Has Domain: Has Range: Version: biologicalEntityRemarks-2011-07-04 Replaces: Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Notes Term Name: associatedBiologicalEntities Identifier: http://rs.tdwg.org/dwc/terms/associatedBiologicalEntities Namespace: http://rs.tdwg.org/dwc/terms/ Label: associatedBiologicalEntities Definition: A list (concatenated and separated) of identifiers of other BiologicalEntity records and their associations to this BiologicalEntity. Comment: Example: "sibling of MXA-231; sibling of MXA-232". For discussion see http://code.google.com/p/darwincore/wiki/BiologicalEntity Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property Refines: Status: recommended Date Issued: 2011-07-04 Date Modified: 2011-07-04 Has Domain: Has Range: Version: associatedBiologicalEntities-2011-07-04 Replaces: associatedOccurrences-2009-04-24 Is Replaced By: Class: http://rs.tdwg.org/dwc/terms/BiologicalEntity ABCD 2.06: DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceInstitutionCode + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitSourceName + DataSets/DataSet/Units/Unit/Associations/UnitAssociation/AssociatedUnitID Terms to be organized under biologicalEntity rather than Occurrence: previousIdentifications associatedMedia associatedReferences

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Re: [tdwg-content] New term needs resolution: yearOfPublication
by Kevin Richards 20 Jul '11

20 Jul '11

Ha. I had the same problem - first time I have had it - is there something dodgy about goo.gl sort links maybe. I got around it by going to unshorten.com and unshortening it. Kevin ----- Reply message ----- From: "Peter Desmet" <peter.desmet(a)umontreal.ca> Date: Wed, Jul 6, 2011 12:46 pm Subject: [tdwg-content] New term needs resolution: yearOfPublication To: "tuco(a)berkeley.edu" <tuco(a)berkeley.edu> Cc: "TDWG Content Mailing List" <tdwg-content(a)lists.tdwg.org> The shortlink http://goo.gl/8WkJa has been disabled (at least on my computer), can you include the full URL to the issue? On Tue, Jul 5, 2011 at 05:24, John Wieczorek <tuco(a)berkeley.edu> wrote: > Looks like this one is off to a good start. If there is no dissenting > opinion in the next 30 days, it looks like it'll be included. > > On Mon, Jul 4, 2011 at 6:00 PM, Peter DeVries <pete.devries(a)gmail.com> wrote: >> I have something similar that I use for stating the year the species was >> described. >> This is useful for sorting by year etc. So +1 >> Note the datatype rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear" >> >> >> From http://lod.taxonconcept.org/ses/v6n7p.html RDF http://10.10.10.122:3000/ses/v6n7p.rdf >> <txn:yearDescribed >> rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">1771</txn:yearDescribed> >> >> Ontology >>  >> <owl:DatatypeProperty >> rdf:about="http://lod.taxonconcept.org/ontology/txn.owl#yearDescribed"> >> <rdfs:label >> rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">yearDes ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

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New Term needs resolution: DigitalStillImage
by John Wieczorek 14 Jul '11

14 Jul '11

Darwin Core Issue 68: http://goo.gl/Q7TRn This term has undergone extensive public commentary since January 2010 when it was first proposed. I will do my best to summarize the thinking on these issues, but please see the full corpus of discussions on tdwg-content to see the full history. It has been suggested that DigitalStillImage is not necessary as a Darwin Core Type vocabulary term (one of the controlled vocabulary terms for basisOfRecord) for at least two reasons: 1) Dublic Core comments on StillImage (http://dublincore.org/documents/dcmi-type-vocabulary/) as: "Note that Image may include both electronic and physical representations." 2) The basisOfRecord term has no real purpose and without it, there was no need for DigitalStillImage as one of its controlled values. The context for the second statement was the use of Darwin Core in RDF. The basisOfRecord term is essential in data sharing mechanisms such as in Simple Darwin Core text files or Darwin Core Archives where there is no other way to express what is the fundamental concept for a record. The impetus for proposing DigitalStillImage was to allow the basisOfRecord to show that the evidence for an Occurrence was based on a digital image (similar to a PreservedSpecimen being evidence). This purpose still has merit. Discussions on DigitalStillImage touched on many other issues related to ontology and missing or inferred Classes in the Darwin Core. To achieve the original goal behind DigitalStillImage for RDF is more complicated and involves the idea of a Class to represent a concept that could be described as "Evidence". I will create a separate thread for the continuation of that discussion, reserving this thread for the closure of the issue of having no way currently to express that a digital image is the basis for a Darwin Core resource. To achieve the original goal for the case of non-RDF data sharing mechanisms, I propose that StillImage be added to the list of recommendations for the Darwin Core Type Vocabulary, along with MovingImage and Sound. Doing so will create no backward incompatibilities in the Darwin Core.

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Re: [tdwg-content] New terms need resolution: "Individual"
by Gregor Hagedorn 12 Jul '11

12 Jul '11

On 11 July 2011 02:51, Paul Murray <pmurray(a)anbg.gov.au> wrote: > What happened to 'Organism'? Would exclude viruses. -- Gregor

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New terms need resolution: geo:lat and geo:long
by John Wieczorek 12 Jul '11

12 Jul '11

Darwin Core Issues 82: http://goo.gl/XhxM This issue arose in discussions on the tdwg-tag list (http://lists.tdwg.org/pipermail/tdwg-tag/2010-August/000050.html) to which not everyone here has access. The issue tracker entry (URL above) summarizes the proposed solution to the problem, which is to re-use the W3C standard geographic coordinate terms geo:lat and geo:long from the namespace "http://www.w3.org/2003/01/geo/wgs84_pos#. These terms would be added as recommended terms organized within the Location class. They would not replace the existing terms dwc:decimalLatitude and dwc:decimalLongitude, which are not the same except under one special circumstance - that the dwc:geodeticDatum is WGS84 (or equivalent). Since this is not always the case, the existing Darwin Core terms cannot be omitted. Open Issues: Determine if there is any objection to include these two terms as recommended terms to use in the Darwin Core.

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New term resolution: dcterms:source
by John Wieczorek 09 Jul '11

09 Jul '11

Darwin Core Issues 96: http://goo.gl/gOkAs This issue has not been subject to public commentary. The proposal seeks to add the term source from the Dublin Core vocabulary to the recommended record-level terms for the Darwin Core. Open Issues: Determine if there is demand for this term from more than one "independent" party. I consider myself an independent party on behalf of VertNet, for which this term woud be a more general solution than the existing Darwin Core term dwc:occurrenceDetails, as it could apply to records of any Class rather than just for Occurrence. Determine if there is any objection to include this term as recommended for use in the Darwin Core. Determine if there is any objection to deprecating dwc:occurrenceDetails in favor of dcterms:source. Here are the descriptions for the two terms for easy comparison: dwc:occurrenceDetails - definition: "A reference (publication, URI) to the most detailed information available about the Occurrence." comment: "Example: "http://mvzarctos.berkeley.edu/guid/MVZ:Mamm:165861". For discussion see http://code.google.com/p/darwincore/wiki/Occurrence" dcterms:source - definition: "A related resource from which the described resource is derived." comment: "The described resource may be derived from the related resource in whole or in part. Recommended best practice is to identify the related resource by means of a string conforming to a formal identification system."

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New term needs resolution: yearOfPublication
by John Wieczorek 06 Jul '11

06 Jul '11

Darwin Core Issue 84: http://goo.gl/8WkJa This issue has not undergone public commentary. Open Issues: Determine if there is a demand for this term. Though the term is well-described in the issue tracker, there is no evidence of a real-world need for it. There has to be a demonstrated need from more than one "independent" source for a term to enter into consideration for addition to the Darwin Core.

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