tdwg / dwc Goto Github PK

Migrate old issues from Google Code to GitHub:

1. Ignore open issues (see #14) and issues with the labels component:DwcaReader and component:DwcaValidator
2. Migrate issues (this tool might help)
3. Optional: reference new issue in old issue, so users can follow up from there.

Cleanup can only be done after initial migration to GitHub (cause we want a release first), see #16.

• Other way to store versions (2009-02-12 to 2013-10-22)
• Rename DarwinCore_files into styles, media or similar (deferred to Issue #20)
• Find a way to host the files from https://code.google.com/p/darwincore/downloads/list

Add more...

Reported by @cgendreau: links in http://rs.tdwg.org/dwc/terms/history/decisions/index.htm are broken, e.g. http://rs.tdwg.org/dwc/terms/history/decisions/Decision-2013-10-09_12

To be fixed after migration

The DwC website should be generated from the RDF document (#17) and markdown files. For the second part, the HTML pages need to be translated to Markdown first (use pandoc).

• http://rs.tdwg.org/dwc/index.htm: index.html
• http://rs.tdwg.org/dwc/terms/index.htm → terms/index.html: will be generated
• http://rs.tdwg.org/dwc/terms/simple/index.htm: simple_dwc.html
• http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm → deprecated
• http://rs.tdwg.org/dwc/terms/namespace/index.htm: change_policy.html
• http://rs.tdwg.org/dwc/terms/guides/xml/index.htm: guides/xml/index.html
• http://rs.tdwg.org/dwc/terms/guides/text/index.htm: guides/text/index.html
• http://rs.tdwg.org/dwc/terms/history/index.htm → terms/history.html: will be generated
• http://rs.tdwg.org/dwc/terms/history/decisions/index.htm: terms/decisions.html
• http://rs.tdwg.org/dwc/terms/history/dwctoabcd/index.htm: terms/mappings.html
• http://rs.tdwg.org/dwc/terms/history/versions/index.htm: deprecated?
• http://rs.tdwg.org/dwc/translations/index.htm: deprecated?

1. Move code to GitHub (#16)
2. Create a single normative RDF document (including current terms and history)
3. Develop a Python(?) script to generate the HTML term page(s) from the normative document. The pages are: http://rs.tdwg.org/dwc/terms/index.htm and http://rs.tdwg.org/dwc/terms/history/index.htm (and maybe others).
4. Generate document and see if it provides the same functionality as the current page
5. Test by making a change to the normative document and see if the page creates correctly. The script should throw relevant error messages.
6. Document how to use the script (including requirements).

Was https://code.google.com/p/darwincore/issues/detail?id=146

New Term

Submitter: David Remsen
Justification: For many insect groups, and perhaps for other taxa, there are a number of important intermediate taxon ranks between Family and Genus. While the higher taxon groupings (Kingdom-Order) also can be subcategorized with sub- and super- intermediates, the use of subfamily is intended to record a finer grade classification than is now possible with the existing terms.
Proponents: iDigBio, World Flora Online, Catalogue of Life, Canadensys
Definition: The full scientific name of the subfamily in which the taxon is classified.
Comment:
Examples: Periptyctinae, Orchidoideae, Sphindociinae
Refines: None
Replaces: None
ABCD 2.06: /DataSets/DataSet/Units/Unit/Identifications/Identification/Result/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonName with /DataSets/DataSet/Units/Unit/Identifications/Identification/Result/TaxonIdentified/HigherTaxa/HigherTaxon/HigherTaxonRank == "subfamilia"

Oct 3, 2013 comment #5 gtuco.btuco
I would like to promote the adoption of the concept mentioned in this issue. To do so, I will need a stronger proposal demonstrating the need to share this information - that is, that independent groups, organizations, projects have the same need and can reach a consensus proposal about how the term should be used. It might be a good idea to circulate the proposal on tdwg-content and see if a community can be built around and support the addition.

Currently recommendations for best practice are placed inconsistently between term definitions and term comments. This proposal is to move all recommendations for how to encode content from definitions to comments. The affected terms would be as follow:

datasetID
occurrenceID
sex
lifeStage
reproductiveCondition
behavior
establishmentMeans
occurrenceStatus
organismID
organismScope
materialSampleID
eventID
eventDate
eventTime
locationID
higherGeographyID
continent
waterBody
islandGroup
island
country
countryCode
municipality
locality
minimumDistanceAboveSurfaceInMeters
maximumDistanceAboveSurfaceInMeters
locationAccordingTo
decimalLatitude
decimalLongitude
geodeticDatum
coordinateUncertaintyInMeters
pointRadiusSpatialFit
verbatimCoordinates
verbatimLatitude
verbatimLongitude
verbatimCoordinateSystem
verbatimSRS
footprintWKT
footprintSRS
footprintSpatialFit
georeferencedDate
georeferenceVerificationStatus
geologicalContextID
identificationID
dateIdentified
identificationVerificationStatus
taxonID
scientificName
subgenus
taxonRank
nomenclaturalCode
taxonomicStatus
measurementID
measurementType
measurementUnit
measurementDeterminedDate
relationshipOfResource
relationshipEstablishedDate

while the following terms already have the recommendations in the comments:

institutionID
collectionID
basisOfRecord
dynamicProperties
recordedBy
preparations
disposition
associatedMedia
associatedReferences
associatedSequences
associatedTaxa
otherCatalogNumbers
associatedOccurrences
associatedOrganisms
previousIdentifications
higherGeography
georeferencedBy
georeferenceSources
typeStatus
identifiedBy
identificationReferences
higherClassification
measurementDeterminedBy

Was https://code.google.com/p/darwincore/issues/detail?id=179

Look at Wikipedia and make sure the documentation there is up-to-date and that the references go both directions, making clean articles with no warnings.

Was https://code.google.com/p/darwincore/issues/detail?id=149

==New Term Recommendation==
Submitter: David Remsen

Justification: In botany, sections are typically used to help organise very large genera, which may have hundreds of species.[1] A botanist wanting to distinguish groups of species may prefer to create a taxon at the rank of section or series to avoid making new combinations

Definition: "The full scientific name of the section in which the taxon is classified."

Comment: Examples: "Anthurium sect. Gymnopodium", "Rhododendron sect. Pentanthera"

Refines: http://rs.tdwg.org/dwc/terms/family

Has Domain: http://rs.tdwg.org/dwc/terms/index.htm#Taxon

Has Range:

Replaces:

ABCD 2.06:

Mar 9, 2012 comment #1 dpremsen
I know I introduced this term but I suppose that it could arguably be covered by including it in the dwc:scientificName.

Mar 9, 2012 comment #3 dpremsen
Would like to amend the definition ""The full scientific name of the (botanical) section in which the taxon is classified. In botany, the section falls below genus but above species. The subgenus, if present, is higher than the section."

Oct 3, 2013 comment #8 gtuco.btuco
I would like to promote the adoption of the concept mentioned in this issue. To do so, I will need a stronger proposal demonstrating the need to share this information - that is, that independent groups, organizations, projects have the same need and can reach a consensus proposal about how the term should be used. It might be a good idea to circulate the proposal on tdwg-content and see if a community can be built around and support the addition.

Was https://code.google.com/p/darwincore/issues/detail?id=147

==New Term Recommendation==
Submitter: David Remsen

Justification: Many taxa belong to large taxonomic families, particularly among the insects but also among other animal and plant groups. Often the 'interesting' components of the classification are operating at the sub-familial-and-below level. In order to effectively capture this more refined classification information, I recommend the addition of tribe (and sub-tribe).

Definition: The full scientific name of the tribe in which the taxon is classified.

Comment: Examples "Ortaliini", "Arethuseae"

Refines:dwc:Family

Has Domain: http://rs.tdwg.org/dwc/terms/Taxon

Has Range:

Replaces:

ABCD 2.06:

Oct 3, 2013 comment #5 gtuco.btuco
I would like to promote the adoption of the concept mentioned in this issue. To do so, I will need a stronger proposal demonstrating the need to share this information - that is, that independent groups, organizations, projects have the same need and can reach a consensus proposal about how the term should be used. It might be a good idea to circulate the proposal on tdwg-content and see if a community can be built around and support the addition.

• Submitter: John Wieczorek on behalf of the May 2013 GBIF hackathon-workshop on Darwin Core and sample data
• Justification (why is this term necessary?): see "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" at http://www.gbif.org/orc/?doc_id=5424
• Proponents (at least two independent parties who need this term): see "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" at http://www.gbif.org/orc/?doc_id=5424.

Proposed attributes of the new term:

• Term name (in lowerCamelCase): environmentalMaterial
• Class (e.g. Location, Taxon): Event
• Definition of the term: The medium or part of the medium of an environmental system.
• Usage comments (recommendations regarding content, etc.): Recommended best practice is to use a controlled vocabulary such as the set of subclasses of the environmental material class (http://purl.obolibrary.org/obo/ENVO_00010483) of the Environment Ontology (ENVO). Values are to represent media as being composed primarily of the named entity, rather than restricted entirely to that entity. For example, "envo:liquid water" is to be understood as "environmental material composed primarily of some chebi:water" in liquid form.
• Examples: envo:soil, envo:sediment, envo:saline water
• Refines (identifier of the broader term this term refines, if applicable):
• Replaces (identifier of the existing term that would be deprecated and replaced by this term, if applicable):
• ABCD 2.06 (XPATH of the equivalent term in ABCD, if applicable): not in ABCD

Original first comment:

Was https://code.google.com/p/darwincore/issues/detail?id=191

Reported by gtuco.btuco, Sep 25, 2013

==New Term Recommendation==

Submitter: John Wieczorek on behalf of the May 2013 GBIF hackathon-workshop on Darwin Core and sample data

Justification: see "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" at http://www.gbif.org/orc/?doc_id=5424

Term Name: environmental material
Identifier: http://purl.obolibrary.org/obo/ENVO_00010483
Namespace: http://purl.obolibrary.org/obo/
Label: Environmental Material
Definition: Material in or on which organisms may live.
Comment: Examples: "scum", "http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see https://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2013-09-25
Date Modified: 2013-09-25
Has Domain:
Has Range:
Refines:
Version: http://purl.obolibrary.org/obo/ENVO_00010483
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

Sep 26, 2013 #1 gtuco.btuco
Based on initial discussions on tdwg-content, modified the proposal to make a new DwC property term that recommends the ENVO class as the range, as follows:

Term Name: environmentalMaterial
Identifier: http://rs.tdwg.org/dwc/terms/environmentalMaterial
Namespace: http://rs.tdwg.org/dwc/terms/
Label: Environmental Material
Definition: Material in or on which organisms may live. Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO).
Comment: Examples: "scum",
"http://purl.obolibrary.org/obo/ENVO_00003930". For discussion see https://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified)
Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
Refines:
Status: proposed
Date Issued: 2013-09-26
Date Modified: 2013-09-26
Has Domain:
Has Range:
Refines:
Version: environmentalMaterial-2013-09-26
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

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.

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/ 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

Look up what was decided by Exec.

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.

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

Migrate the open issues from Google Code to GitHub:

1. Assess if issue is still relevant, close if not.
2. Migrate open issues (this tool might help)
3. Reference new issue in old issue, so users can follow up from there and close.
4. Document this process (will be useful for other migrations, e.g. GBIF repos)

Template for closing issue:

The Darwin Core code, documentation and issues have been migrated to GitHub. If you want to keep receiving updates regarding this issue, go to https://github.com/tdwg/dwc/issues/xx and click subscribe. You will need to create a GitHub account if you don't have one yet.

Currently the web pages documenting the Darwin Core terms include references to documentation for those terms outside the standard. This is done by adding a sentence such as "For discussion see http://terms.tdwg.org/wiki/dwc:basisOfRecord." These references do not appear anywhere in the normative RDF.

This proposal is to add dcterms:references with the URL to the external documentation into the term defnitions in RDF to aid in the management of the standard and its associated documentation directly from the normative document, and to show the references in their own property in the human-friendly documentation rather than appended to the end of the comments.

If accepted, for example, the RDF declaration of the basisOfRecord term would change from

    <rdf:Description rdf:about="http://rs.tdwg.org/dwc/terms/basisOfRecord">
        <rdfs:label xml:lang="en">Basis of Record</rdfs:label>
        <rdfs:comment xml:lang="en">The specific nature of the data record.</rdfs:comment>
        <dcterms:description xml:lang="en">Recommended best practice is to use a controlled vocabulary such as the list of Darwin Core classes. Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"</dcterms:description>
        <rdfs:isDefinedBy rdf:resource="http://rs.tdwg.org/dwc/terms/"/>
        <dcterms:issued>2008-11-19</dcterms:issued>
        <dcterms:modified>2014-10-23</dcterms:modified>
        <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"/>
        <dcterms:hasVersion rdf:resource="http://rs.tdwg.org/dwc/terms/history/#basisOfRecord-2014-10-23"/>
        <dcterms:replaces rdf:resource="http://rs.tdwg.org/dwc/terms/basisOfRecord-2009-12-07"/>
        <dwcattributes:status>recommended</dwcattributes:status>
        <dwcattributes:decision rdf:resource="http://rs.tdwg.org/dwc/terms/history/decisions/#Decision-2014-10-26_15"/>
        <dwcattributes:abcdEquivalence>DataSets/DataSet/Units/Unit/RecordBasis</dwcattributes:abcdEquivalence>
        <dwcattributes:organizedInClass rdf:resource="all"/>
    </rdf:Description>

to

    <rdf:Description rdf:about="http://rs.tdwg.org/dwc/terms/basisOfRecord">
        <rdfs:label xml:lang="en">Basis of Record</rdfs:label>
        <rdfs:comment xml:lang="en">The specific nature of the data record.</rdfs:comment>
        <dcterms:description xml:lang="en">Recommended best practice is to use a controlled vocabulary such as the list of Darwin Core classes. Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation"</dcterms:description>
        <rdfs:isDefinedBy rdf:resource="http://rs.tdwg.org/dwc/terms/"/>
        <dcterms:issued>2008-11-19</dcterms:issued>
        <dcterms:modified>2014-10-23</dcterms:modified>
        <dcterms:references>http://terms.tdwg.org/wiki/dwc:basisOfRecord</dcterms:references>
        <rdf:type rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#Property"/>
        <dcterms:hasVersion rdf:resource="http://rs.tdwg.org/dwc/terms/history/#basisOfRecord-2014-10-23"/>
        <dcterms:replaces rdf:resource="http://rs.tdwg.org/dwc/terms/basisOfRecord-2009-12-07"/>
        <dwcattributes:status>recommended</dwcattributes:status>
        <dwcattributes:decision rdf:resource="http://rs.tdwg.org/dwc/terms/history/decisions/#Decision-2014-10-26_15"/>
        <dwcattributes:abcdEquivalence>DataSets/DataSet/Units/Unit/RecordBasis</dwcattributes:abcdEquivalence>
        <dwcattributes:organizedInClass rdf:resource="all"/>
    </rdf:Description>

And the relevant part of the human-friendly documentation for basisOfRecord would change from

Identifier:   http://rs.tdwg.org/dwc/terms/basisOfRecord
Definition:  The specific nature of the data record.
Comment:  Recommended best practice is to use a controlled vocabulary such as the list of Darwin Core classes. Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation". For discussion see http://terms.tdwg.org/wiki/dwc:basisOfRecord

to

Identifier:   http://rs.tdwg.org/dwc/terms/basisOfRecord
Definition:  The specific nature of the data record.
Comment:  Recommended best practice is to use a controlled vocabulary such as the list of Darwin Core classes. Examples: "PreservedSpecimen", "FossilSpecimen", "LivingSpecimen", "HumanObservation", "MachineObservation". 
References: http://terms.tdwg.org/wiki/dwc:basisOfRecord

Was https://code.google.com/p/darwincore/issues/detail?id=177.

The Darwin Core Type vocabulary was deprecated as of 2014-10-26 (http://rs.tdwg.org/dwc/terms/history/decisions/index.htm#Decision-2014-10-26_15). One of the type vocabulary terms, NomenclaturalChecklist (http://rs.tdwg.org/dwc/terms/history/index.htm#NomenclaturalChecklist-2009-01-23), was not replaced by an equivalent in the remaining Darwin Core namespace (http://rs.tdwg.org/dwc/terms/). Yet there is a perceived need for a category of Taxon (http://rs.tdwg.org/dwc/terms/index.htm#Taxon) that is more specific than the whole set of types of records that might be shared in a Taxon record. The proposed term, ScientificName, would fulfill that role for Taxon records that are only about scientific names rather than taxon concepts, for example. The specific proposal is to add the class ScientificName as described below. This term would then become available among those recommended for use as values of the basisOfRecord term (http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord).

Term Name: ScientificName
Identifier: http://rs.tdwg.org/dwc/terms/ScientificName
Namespace: http:/rs.tdwg.org/dwc/terms
Label: Scientific Name
Definition: A scientific name.
Comment: Example: A scientific name with full authorship information.
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: recommended
Date Issued: 2014-10-23
Date Modified: 2014-11-12
Has Domain:
Has Range:
Version: ScientificName-2014-11-12
Replaces: http://rs.tdwg.org/dwc/dwctype/NomenclaturalChecklist
IsReplacedBy:
Class:
ABCD 2.0.6: not in ABCD

Further considerations: The documentation would have to be updated wherever the classes are listed.

Was https://code.google.com/p/darwincore/issues/detail?id=178

Reported by gtuco.btuco, May 23, 2013
Consider adoption of the GSC/ENVO material, feature, and biome environment terms in place of dwc:habitat

http://bioportal.bioontology.org/ontologies/50201?p=terms

May 23, 2013 comment #1 gtuco.btuco
Alternative suggestion is to maintain the term and in Event-based Darwin Core records, put habitat information into a one-to-many MeasurementOrFact, potentially with a new property for the authority for the value of the MeasurementOrFact to show what vocabulary was being used.

Sep 25, 2013 comment #2 gtuco.btuco
As a result of the workshop findings "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" published at http://www.gbif.org/orc/?doc_id=5424, it was proposed that the Darwin Core Standard adopt four classes from ENVO, namely, habitat (http://purl.obolibrary.org/obo/ENVO_00002036), biome (http://purl.obolibrary.org/obo/ENVO_00000428), environmental feature (http://purl.obolibrary.org/obo/ENVO_00002297), and environmental material (http://purl.obolibrary.org/obo/ENVO_00010483).

As a result of the workshop, the following proposal for changes to the habitat term were posted to the tdwg-content list (see http://lists.tdwg.org/pipermail/tdwg-content/2013-September/003066.html):

Term Name: habitat
Identifier: http://purl.obolibrary.org/obo/ENVO_00002036
Namespace: http://purl.obolibrary.org/obo/
Label: Habitat
Definition: A spatial region having environmental qualities which may sustain an organism or a community of organisms.
Comment: Examples: "freshwater habitat", "http://purl.obolibrary.org/obo/ENVO_00002037". For discussion see https://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2008-11-19
Date Modified: 2013-09-25
Has Domain:
Has Range:
Refines:
Version: http://purl.obolibrary.org/obo/ENVO_00002036
Replaces: habitat-2009-04-24
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

Feb 6, 2014 comment #3 eotuama.gbif
The GBIF Hackathon workshop recommended that DwC adopt the four EnvO classes (habitat, biome, environental feature, environmental material) as values for appropriate DwC properties. Thus the existing dwc:habitat property would have its permitted values restricted to the members from the EnvO Habitat class (e.g., freshwater habitat, http://purl.obolibrary.org/obo/ENVO_00002037). Three new DwC properties, namely, "biome", "environmentalFeature", "environmentalMaterial" would need to be created to hold values from the equivalent EnvO classes.

Feb 6, 2014 comment #4 wixner
Agree it makes sense to have those 3 new terms in Darwin Core, we would need a separate request for each of them if that should become real.

Looking at the EnvO biome class though I am not convinced EnvO is the clear best vocabulary to recommend for biomes. They simply refer to outdated wikipedia definitions. If you look into the current wikipedia article they already have various important concurrent classification schemes listed and described: http://en.wikipedia.org/wiki/Biome#Biome_classification_schemes

I do not feel confident enough to pick one in particular. It would be good to know who actually is using these schemes a) when managing taxon occurrences and b) when classifying the worlds surface. NASA has a project for the later and they follow a different scheme: http://earthobservatory.nasa.gov/Experiments/Biome/

Was https://code.google.com/p/darwincore/issues/detail?id=148

==New Term Recommendation==
Submitter: David Remsen

Justification: Many taxa belong to large taxonomic families, particularly among the insects but also among other animal and plant groups. Often the 'interesting' components of the classification are operating at the sub-familial-and-below level. In order to effectively capture this more refined classification information, I recommend the addition of tribe (and sub-tribe).

Definition: "The full scientific name of the sub-tribe in which the taxon is classified."

Comment: Examples: "Plotinini", "Typhaeini"

Refines:http://rs.tdwg.org/dwc/terms/index.htm#family

Has Domain: http://rs.tdwg.org/dwc/terms/Taxon

Has Range:

Replaces:

ABCD 2.06:

Oct 3, 2013 Delete comment Project Member #5 gtuco.btuco
I would like to promote the adoption of the concept mentioned in this issue. To do so, I will need a stronger proposal demonstrating the need to share this information - that is, that independent groups, organizations, projects have the same need and can reach a consensus proposal about how the term should be used. It might be a good idea to circulate the proposal on tdwg-content and see if a community can be built around and support the addition.

Migrate Darwin Core code to GitHub

1. Migrate SVN repo to git (locally). There should be tools for this.
2. Push all code to GitHub
3. Create release (as an archive)
4. Clean up code to remove irrelevant elements (see #19)
5. Document this process (will be useful for other migrations, e.g. GBIF repos)

Was https://code.google.com/p/darwincore/issues/detail?id=198

Reported by [email protected], Nov 28, 2013

Term Name:LifeStage
This issue is linked with issue 36.
The definition of lifeStage is "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."
The example add the possibility to add the count : "2 adults 4 juveniles"

So the example extend the definition of the term (2 notions) : life stage and count.

Recommendation:
My recommandation is to make that one term refers to one and only one notion to make the data easier to reuse.
If this information on count of individual by life stage is important : it needs to be exchange in its own term like "AdultCount", "JuvenilCount" or another way to stock this information must be created.

If only the global count is needed, I think people should use the terms IndividualCount = 6 ; and lifeStage :" adult juvenile"

If this change is not possible, I think it's important to make the definition and the example congruent : erase the example on the count on lifeStage or extend the definition with the possibility to add count. This last option seems to be the worst to make easier the reuse of the data.

Submitter: Julie Chataigner jchataig@mnhn

Nov 29, 2013 comment #1 wixner
Fully support this. Darwin Core should recommend simple values for terms where possible and avoid using a single term for complex data. For lifeStage I would follow Julies recommendation and only list life stages and if individualCount is given it should be for all individuals no matter which sex or life stage they have. It might be worth to recommend to use the measurements and facts extension for the detailed breakdown if one wishes to publish counts per sex and/or life stage

Dec 3, 2013 comment #2 gtuco.btuco
I also agree.

The example for dynamicProperties includes the following JSON:

{'heightInMeters':'1.5'}
{'tragusLengthInMeters':'0.014', 'weightInGrams':'120'}
{'natureOfID':'expert identification', 'identificationEvidence':'cytochrome B sequence'}
{'relativeHumidity':'28', 'airTemperatureInCelcius':'22', 'sampleSizeInKilograms':'10'}{'aspectHeading':'277', 'slopeInDegrees':'6'}
{'iucnStatus':'vulnerable', 'taxonDistribution':'Neuquén, Argentina'}

JSON requires strings to be in double quotes, while the example shows single quotes. That's probably because every example is in double quotes - it would be better to have those as inline code, but that's another issue - but it's wrong none the less.

Why are all the numbers in quotes? Numbers don't require those. So, I would suggest to update the example to:

Examples: "{"heightInMeters":1.5}", "{"tragusLengthInMeters":0.014, "weightInGrams":120}", "{"natureOfID":"expert identification", "identificationEvidence":"cytochrome B sequence"}", "{"relativeHumidity":28, "airTemperatureInCelcius":22, "sampleSizeInKilograms":10}", "{"aspectHeading":277, "slopeInDegrees":6}", "{"iucnStatus":"vulnerable", "taxonDistribution":"Neuquén, Argentina"}". For discussion see http://terms.tdwg.org/wiki/dwc:dynamicProperties

New Term

Submitter: Markus Döring
Justification: Clear separation of the type status and the typified scientific name that is typified by a type specimen, the subject. Looking at how dwc:typeStatus has been used in all of GBIFs specimen data one can see there is the need to express this, but it should better be handled with a term on its own and leave typeStatus for the status of the type only. The term name itself is also used by ABCD: http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcept0603
Organized in Class (e.g., Occurrence, Event, Location, Taxon): Identification
Definition: Scientific name of which Organism is a nomenclatural type.
Comment: It is recommended to also indicate the typeStatus of the Organism.
Refines: None
Replaces: None
ABCD 2.06:
DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/TypifiedName

Original comment:

Was https://code.google.com/p/darwincore/issues/detail?id=197

==New Term Recommendation==
Submitter:
Markus Döring

Justification:
Clear separation of the type status and the typified scientific name that is typified by a type specimen, the subject. Looking at how dwc:typeStatus has been used in all of GBIFs specimen data one can see there is the need to express this, but it should better be handled with a term on its own and leave typeStatus for the status of the type only. The term name itself is also used by ABCD: http://wiki.tdwg.org/twiki/bin/view/ABCD/AbcdConcept0603

Definition:
The scientific name that is based on the type specimen.

Comment:
It is recommended to also indicate the typeStatus of the specimen.

Refines:

Has Domain:

Has Range:

Replaces:

ABCD 2.06:
DataSets/DataSet/Units/Unit/SpecimenUnit/NomenclaturalTypeDesignations/NomenclaturalTypeDesignation/TypifiedName

A typical example how typeStatus is used currently is:

ISOTYPE of Polysiphonia amphibolis Womersley

which we could express much better with 2 terms:

dwc:typeStatus=ISOTYPE
dwc:typifiedName=Polysiphonia amphibolis Womersley

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.

Definition

A number or enumeration value for the quantity of organisms. Use with organismQuantityType to indicate the type of entity that is being quantified.

Comment

The terms organismQuantity and organismQuantityType are required to be used as a pair. The value of organismQuantity is a number or enumeration, e.g., “27” for an organismQuantityType “individuals”, “12.5” for an organismQuantityType “%biomass”, or “r” for an organismQuantityType “BraunBlanquetScale”.

Term group

Occurrence

Was https://code.google.com/p/darwincore/issues/detail?id=180

Reported by gtuco.btuco, May 24, 2013
==Documentation Error Report==
URL:
http://rs.tdwg.org/dwc/terms/guides/text/index.htm

Error description:
Not actually an error, just a request to make a recommendation that isn't there already. The Darwin Core Text Guide does not make recommendations about the metadata document.

Recommended remedy:
Add a recommendation about the metadata in the archive, that it conform minimally to a standard, for example Dublin Core Application Profile.

Submitter: John Wieczorek, Markus Döring

Add a references attribute to the RDF. For one, it would contain the link to the secondary documentation, which would be removed from the comment field on the website.

From:

Identifier:   http://purl.org/dc/terms/rightsHolder
Class:    all
Definition:  A person or organization owning or managing rights over the resource.
Comment: Example: "The Regents of the University of California.". For discussion see http://code.google.com/p/darwincore/wiki/RecordLevelTerms
Details:      http://dublincore.org/documents/dcmi-terms/#terms-rightsHolder, dcterms:rightsHolder

To:

Identifier:   http://purl.org/dc/terms/rightsHolder
Class:    all
Definition:  A person or organization owning or managing rights over the resource.
Comment: Example: "The Regents of the University of California.".
References:      http://code.google.com/p/darwincore/wiki/RecordLevelTerms
Details:      http://dublincore.org/documents/dcmi-terms/#terms-rightsHolder, dcterms:rightsHolder

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

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

Looking into the GBIF data it appears that dwc:preparations is used to capture 2 distinct pieces of information, the preservation method and the part of the organism being stored.

ABCD has a related concept KindOfUnit defined as:

Part(s), physical state, or class of materials represented by this specimen.

organismPart definition

Part(s) or class of materials represented by an organism.
Recommended best practice is to use a controlled vocabulary.

Examples:

whole organisms, antlers, bark, blood samples, bones, eggs, feathers, fruits, galls, heads, leaves

For @tucotuco:

• Review current issue templates (the ones that are in use)
• Review status labels
• Add the ones we want to keep as labels to the GitHub issues
• Write/transfer templates to CONTRIBUTING

For @peterdesmet:

• Look for GitHub special file that informs contributors.
• Add file to this repository

Was
https://code.google.com/p/darwincore/issues/detail?id=236 and
https://code.google.com/p/darwincore/issues/detail?id=239 and
https://code.google.com/p/darwincore/issues/detail?id=241

When the MaterialSample proposal was ratified, no consideration had been given to which existing terms might be organized in this new class. Three terms (preparations, associatedSequences, and disposition) make sense to "belong in" this class.

==Term Change Recommendation==
Submitter: John Wieczorek

Justification: Previous to the adoption of the MaterialSample class, there was no better class in which to arrange preparations than Occurrence. MaterialSample is the appropriate class in which to arrange preparations.

Term Name: preparations
Reference: http://rs.tdwg.org/dwc/terms/index.htm#preparations
Version: preparations-2009-04-24
Status: deprecated
IsReplacedBy: preparations-2014-10-22

Term Name: preparations
Version: preparations-2014-10-22
Status: recommended
Replaces: preparations-2009-04-24
Class: http://rs.tdwg.org/dwc/terms/MaterialSample

==Term Change Recommendation==
Submitter: John Wieczorek

Justification: Previous to the adoption of the MaterialSample class, there was no better class in which to arrange associatedSequences than Occurrence. MaterialSample is the appropriate class in which to arrange associatedSequences.

Term Name: associatedSequences
Reference: http://rs.tdwg.org/dwc/terms/index.htm#associatedSequences
Version: associatedSequences-2009-04-24
Status: deprecated
Definition: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.
IsReplacedBy: associatedSequences-2014-10-22

Term Name: associatedSequences
Version: associatedSequences-2014-10-22
Status: recommended
Definition: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the MaterialSample.
Replaces: associatedSequences-2009-04-24
Class: http://rs.tdwg.org/dwc/terms/MaterialSample

==Term Change Recommendation==
Submitter: John Wieczorek

Justification: Previous to the adoption of the MaterialSample class, there was no better class in which to arrange disposition than Occurrence. MaterialSample is the appropriate class in which to arrange disposition.

Term Name: disposition
Reference: http://rs.tdwg.org/dwc/terms/index.htm#disposition
Version: disposition-2009-04-24
Status: deprecated
IsReplacedBy: disposition-2014-10-22

Term Name: disposition
Version: disposition-2014-10-22
Status: recommended
Replaces: disposition-2009-04-24
Class: http://rs.tdwg.org/dwc/terms/MaterialSample

The original preferred citation was:

Darwin Core Task Group, Biodiversity Information Standards - TDWG. 2009. Darwin Core.
http://rs.tdwg.org/dwc (accessed 14 Oct 2009).

Which I altered to:

Darwin Core Task Group, Biodiversity Information Standards (TDWG). 2009. Darwin Core. 
http://rs.tdwg.org/dwc/ (accessed on 2014-10-29).

But the broader question is: is this still the preferred citation? If someone wants to reference Darwin Core in a paper, wouldn't it be better to reference: 10.1371/journal.pone.0029715?

Looking into the GBIF data it appears that dwc:preparations is used to capture 2 distinct pieces of information, the preservation method and the part of the organism being stored.

A new term "preservationMethod" is requested to capture the one part. NCD has created a vocabulary for preservation methods in the TDWG ontology that could be used as a recommended vocabulary: http://rs.tdwg.org/ontology/voc/Collection#SpecimenPreservationMethodTypeTerm

preservationMethod definition

The process or technique used to prevent physical deterioration of non-living collections.
Recommended best practice is to use a controlled vocabulary such as the NCD Specimen Preservation Method Type Term vocabulary.

Examples

dried; driedAndPressed; fluidPreserved; frozen; pinned

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

Definition

The type of entity to which the number or enumeration value reported for the quantity of organisms in organismQuantity refers.

Comment

The terms organismQuantity and organismQuantityType are required to be used as a pair. The value of organismQuantityType (i.e., the entity being
measured) is expected to be drawn from a small controlled vocabulary with terms such as “Individuals”, “%Biomass”, “%Biovolume”, “%Species”, “%Coverage”, “BraunBlanquetScale”, “DominScale”. Examples when combined with organismQuantity values: + on DominScale; 5 on BraunBlanquetScale; 45 for %Biomass.

Term group

Occurrence

New Term

Submitter: Markus Döring
Justification: A new term is needed to represent a parsed scientific name of an infrageneric rank, e.g a subgenus. The TDWG ontology defines the exact same concept: http://rs.tdwg.org/ontology/voc/TaxonName.rdf#infragenericEpithet
Proponents: GBIF (already in use), Catalogue of Life (already in use), IPNI (already in use)
Definition: The infrageneric part of a binomial name at ranks above species but below genus.
Comment: The term infragenericEpithet should be used in conjunction with genericName, specificEpithet, infraspecificEpithet, taxonRank and scientificNameAuthorship to represent the individual elements of the complete scientificName. It can be used to indicate the subgenus placement of a species, which in zoology is often given in parentheses. Can also be used to share infrageneric names such as botanical sections (e.g., Vicia sect. Cracca)
Examples: Abacetillus for scientificName Abacetus (Abacetillus) ambiguus, Cracca for scientificName Vicia sect. Cracca
Refines: None
Replaces: None
ABCD 2.06: //DataSets/DataSet/Units/Unit/Identifications/Identification/Result/TaxonIdentified/ScientificName/NameAtomised/Bacterial/Subgenus (bacterial names),
//DataSets/DataSet/Units/Unit/Identifications/Identification/Result/TaxonIdentified/ScientificName/NameAtomised/Zoological/Subgenus (zoological names),
//DataSets/DataSet/Units/Unit/Identifications/Identification/Result/TaxonIdentified/ScientificName/NameAtomised/Botanical/FirstEpithet (botanical names)

Mar 27, 2014 comment #1 [email protected]
Referring to my comment in 227. Doesn't it make more sense to have the subgenus name to be composed of a genericEpithet and an infragenericEpithet, rather than genericName and infragenericEpithet?

Original comment:

Was https://code.google.com/p/darwincore/issues/detail?id=228

==New Term Recommendation==
Submitter: Markus Döring

Justification: A new term is needed to represent a parsed scientific name of an infrageneric rank, e.g a subgenus. The TDWG ontology defines the exact same concept: http://rs.tdwg.org/ontology/voc/TaxonName.rdf#infragenericEpithet

Definition: The infrageneric part of a binomial name at ranks above species but below genus. Names at ranks between species and genus are composed of two words; the genus and this infrageneric epithet. This term should therefore usually be accompanied by the genericName term.

Comment:

Refines:

Has Domain:

Has Range:

Replaces:

ABCD 2.06:

Mar 27, 2014 comment #1 [email protected]
Referring to my comment in 227. Doesn't it make more sense to have the subgenus name to be composed of a genericEpithet and an infragenericEpithet, rather than genericName and infragenericEpithet?

Was https://code.google.com/p/darwincore/issues/detail?id=144

Reported by wixner, Mar 6, 2012
Submitter:
Markus Döring

Justification:
scientific names, in particular bacteria, associated with molecular data often contain a strain. These can only be shared now via the full scientificName which is very difficult to be parsed in such cases due to the lack of a syntactic restriction. Some people share the strain via the infraspecificEpithet, but there are strains also for subspecies and the infraspecificEpithet should be reserved for code compliant epithets.

Definition:
The strain name excluding its rank marker, e.g. strain

Comment:
For example "Bacillus thuringiensis subsp.kurstaki Strain HD1" as published in http://aem.asm.org/content/67/3/1035.full could be atomized as:
{{{
genus=Bacillus
speciesEpithet=thuringiensis
taxonRank=subspecies
taxonRankVerbatim=subsp.
infraspecificEpithet=kurstaki
strain=HD1
}}}

Mar 6, 2012 comment #1 wixner
see also issue141 (#41)

Mar 6, 2012 comment #2 pyilmaz.mgx
Yes, strain name would be great to have, as it is an important piece of data for prokaryotes, i.e. for tracking the type strain of the species etc...

Oct 3, 2013 comment #6 gtuco.btuco
I would like to promote the adoption of the concept mentioned in this issue. To do so, I will need a stronger proposal demonstrating the need to share this information - that is, that independent groups, organizations, projects have the same need and can reach a consensus proposal about how the term should be used. It might be a good idea to circulate the proposal on tdwg-content and see if a community can be built around and support the addition.

New term

• Submitter: John Wieczorek on behalf of the May 2013 GBIF hackathon-workshop on Darwin Core and sample data
• Justification (why is this change necessary?): see "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148965/
• Proponents (who needs this change): Genomic Standards Consortium (GSC), Georeferencing Best Practices, also see "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148965/

Proposed new attributes of the term:

• Term name (in lowerCamelCase): biome
• Organized in Class (e.g. Location, Taxon): Event
• Definition of the term: An ecosystem in which the dominant ecological communities have reached their final successional states, forming stable climax communities.
• Usage comments (recommendations regarding content, etc.): Biomes are typically identified by their patterns of ecological succession and climax communities. They are defined by communities of plants, animals, and other organisms which have - by and large - stabilized (i.e., reached a climax successional state) with respect to their prevailing environmental conditions and climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Recommended best practice is to use a controlled vocabulary such as the set of subclasses of the biome class (http://purl.obolibrary.org/obo/ENVO_00000428) of the Environment Ontology (ENVO).
• Examples: tropical moist broadleaf forest biome [ENVO:01000228]
• Refines (identifier of the broader term this term refines, if applicable): None
• Replaces (identifier of the existing term that would be deprecated and replaced by this term, if applicable): None
• ABCD 2.06 (XPATH of the equivalent term in ABCD or EFG, if applicable): not in ABCD

Was https://code.google.com/p/darwincore/issues/detail?id=189

Reported by gtuco.btuco, Sep 25, 2013

==New Term Recommendation==
Submitter: John Wieczorek on behalf of the May 2013 GBIF hackathon-workshop on Darwin Core and sample data

Justification: see "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" at http://www.gbif.org/orc/?doc_id=5424

Term Name: biome
Identifier: http://purl.obolibrary.org/obo/ENVO_00000428
Namespace: http://purl.obolibrary.org/obo/
Label: Biome
Definition: A major class of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and other factors like climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Biomes are often identified with particular patterns of ecological succession and climax vegetation.
Comment: Examples: "flooded grassland biome", "http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see https://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2013-09-25
Date Modified: 2013-09-25
Has Domain:
Has Range:
Refines:
Version: http://purl.obolibrary.org/obo/ENVO_00000428
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

Sep 26, 2013 comment #1 gtuco.btuco
Based on initial discussions on tdwg-content, modified the proposal to make a new DwC property term that recommends the ENVO class as the range, as follows:

Term Name: biome
Identifier: http://rs.tdwg.org/dwc/terms/biome
Namespace: http://rs.tdwg.org/dwc/terms/
Label: Biome
Definition: A major class of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures (such as trees, shrubs, and grasses), leaf types (such as broadleaf and needleleaf), plant spacing (forest, woodland, savanna), and other factors like climate. Unlike ecozones, biomes are not defined by genetic, taxonomic, or historical similarities. Biomes are often identified with particular patterns of ecological succession and climax vegetation. Recommended best practice is to use a controlled vocabulary such as defined by the biome class of the Environment Ontology (ENVO).
Comment: Examples: "flooded grassland biome",
"http://purl.obolibrary.org/obo/ENVO_01000195". For discussion see https://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified)
Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
Refines:
Status: proposed
Date Issued: 2013-09-26
Date Modified: 2013-09-26
Has Domain:
Has Range:
Refines:
Version: biome-2013-09-26
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

Create a CSS file for the HTML pages that will be hosted on gh-pages.

• Should be a separate file
• Based on http://rs.tdwg.org/dwc/DarwinCore_files/default.css
• Could maybe use an update
• We could include CDN bootstrap for some quick nicer styles
• Rename DarwinCore_files drectory to styles. (Was in Issue #19)
• Review assets

Was https://code.google.com/p/darwincore/issues/detail?id=199

Reported by [email protected], Nov 28, 2013

Term Name:Sex
This issue is linked with issue 35.
The definition of sex is "The sex of the biological individual(s) represented in the Occurrence. Recommended best practice is to use a controlled vocabulary."
The example add the possibility to add the count : "8 males, 4 females"

So the example extend the definition of the term (2 notions) : sex and count.

Recommendation:
My recommandation is to make that one term refers to one and only one notion to make the data easier to reuse.
If this information on count of individual by sex is important : it needs to be exchange in its own term like "MaleCount", "FemaleCount" or another way to stock this information must be created.

If only the global count is needed, I think people should use the terms IndividualCount = 12 ; and lifeStage :" M F"

If this change is not possible, I think it's important to make the definition and the example congruent : erase the count example or extend the definition with the possibility to add count. This last option seems to be the worst to make easier the reuse of the data.

Submitter: Julie Chataigner [email protected]

Nov 29, 2013 comment #1 wixner
Fully support this. Darwin Core should recommend simple values for terms where possible and avoid using a single term for complex data. For sex I would follow Julies recommendation and only list different genders. If individualCount is given it should be for all individuals no matter which sex or life stage they have. It might be worth to recommend to use the measurements and facts extension for the detailed breakdown if one wishes to publish counts per sex and/or life stage

Dec 3, 2013 comment #2 gtuco.btuco
I also agree.

We should describe how one can contribute to the standard. This should be done in this file: https://github.com/tdwg/dwc/blob/master/CONTRIBUTING.md

• Documentation error report
• Term change recommendations
• New term requests
• Questions
• Change standards (once #17 is done): change RDF as a pull request

This allows us to have the whole workflow on GitHub. We would need to redirect rs.tdwg.org to http://tdwg.github.io/dwc/ (I have already done such redirects for other websites).

Was https://code.google.com/p/darwincore/issues/detail?id=181

Reported by gtuco.btuco, May 24, 2013
Create a ResourceRelationship extension that allows any record in the core to be related to any other record in the core explicitly. This needs to relax the GUID requirement for the ResourceID.

Was https://code.google.com/p/darwincore/issues/detail?id=232

The rowType is currently optional, defaulting to SimpleDarwinRecord. This should become a required field without a hidden default that no one is looking at.

<xs:attribute name="rowType" type="xs:string" use="optional"default="http://rs.tdwg.org/dwc/xsd/simpledarwincore/SimpleDarwinRecord"/>

Previous commentary:

Submitted by: timrobertson100, Mar 24, 2014

The XSD [1] for the DwC-A does not conform to the standard as described in the Text guide [2].

In the Text guidelines it states that:
"If extensions are being used, the element must contain a element that indicates the column in the extension file that contains the core record identifier (the matching in the core file)."

However, the XSD is as follows (note, it is optional):
<xs:element name="coreid" type="arch:idFieldType" minOccurs="1" maxOccurs="1"/>
…
<xs:complexType name="idFieldType">
<xs:attribute name="index" type="xs:integer" use="optional"/>
/xs:complexType

This is uncovered with Pensoft archives that won't go through the DwC-A Java libraries (reader, validator) which are in widespread use (ALA, SiB colombia, Canadensys, SiB Brazil, DwC-A Validator, IPT, GBIF harvesting tools, GBIF France, GBIF Spain, OBIS etc).

[1] http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd
[2] http://rs.tdwg.org/dwc/terms/guides/text/index.htm#coreTag

Mar 25, 2014 Delete comment #1 Patrick.R.Leary
I'll add some thoughts from my own and EOL's perspectives.

I recommend we modify the standard to explicitly allow empty or missing coreids in extensions.

EOL has been taking advantage of this for years now. Basically this allows people to declare extensions with no relationships at all with the core. This has been incredibly useful for EOL in that we can use the DwC-Text format to express content not limited to a star-schema structure (and ultimately creating systems like TraitBank [1] entirely using DwC-Text archives which are valid according to the current XSD). Wether or not this is a good idea, the fact is this is currently possible. And to 'fix' this problem would prevent this, so it would in essence make DwC-Text far less expressive and would force EOL to adopt a new format.

My take on it is, if there is no coreid in a extension then consumers should feel free to ignore if they don't want it. Furthermore, we're already in this scenario now. If I create a new extension for MyPetNames and link that to a core file of Taxon, this could be valid against the current and 'fixed' DwC-Text, but consumers will happily ignore MyPetNames because no one cares. This 'bug' just allows more of the same. So while this might technically be a bug - I see it as a very useful feature and having little consequence on consumers or providers.

As a developer I am confused by what the 'standard' is we are talking about, and what is technically a 'bug'. It appears the DarwinCore terms and definitions, and the DwC-Text guide, is the 'standard' and the XSD is just documentation - just an example of how one might possibly implement the text guide idea. But if we didn't have the XSD, many different providers may have developed many different XSDs which conform to the description of DwC-Text, yet they could all be incompatible.

So from an interoperability perspective I see DwC-Text as needing a more technical definition (a specific implementation) to point to as the standard. This is different from the bulk of DwC which is just terms and definitions which don't need an implementation to be clearly defined. So maybe its close to time that DwC-Text should be pulled out of DwC, such that the one standard becomes two (or one and a proposed second), and DwC-Text which is far more technical in nature can have its standard definition also be very technical.

This leads to my final though which is, if the bug is in the XSD, and this XSD is just documentation and not the standard, does that mean that TDWG can change the contents of what http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd resolves to without versioning DwC? EOL uses that XSD as that URL and any changes made to it, bug fixes included, could break EOL systems. If we just consider the XSD documentation then maybe EOL has just been using it wrong and we should use our own version, but I would how that as a standards body TDWG would promote standardizing these technical specifications (implementations).

Long story shorter - I think that coreid should not be required as when it is not required there is a lot more that can be done with DwC-Text. And I hope that if the XSD changes the URL will also change. But if it is decided to not version the XSD, then hopefully that can be widely announced so users of the XSD can be given time to update their software.

[1] http://eol.org/traitbank

Was https://code.google.com/p/darwincore/issues/detail?id=152

Reported by wixner, Mar 22, 2012

==New Term Recommendation==
Submitter: Markus Döring

Justification: To complete the capability of darwin core to share atomised names a new term for named hybrids is needed to denote the part of the name that is considered to be a notho taxon. The multiplication symbol used to mark hybrids is not part of the name and therefore should not be used inside the other name terms like specificEpithet. See ICBN H.3A.1. "The multiplication sign ×, indicating the hybrid nature of a taxon, should be placed so as to express that it belongs with the name or epithet but is not actually part of it."

Definition: The part of a name of a notho taxon which is considered to be of hybrid nature. Values allowed are generic, infrageneric, specific or infraspecific only.

Comment: This term is only to be used for named hybrids, not full hybrid formulas. Examples of named hybrids are "generic" for ×Agropogon P. Fourn. (1934); "generic" for ×Agropogon littoralis (Sm.) C. E. Hubb. (1946); "specific" for Salix ×capreola Andersson (1867); "infraspecific" for Polypodium vulgare nothosubsp. mantoniae (Rothm.) Schidlay

Refines:

Has Domain:

Has Range:

Replaces:

ABCD 2.06:

Mar 23, 2012 comment #1 peter.desmet.cubc
Markus, could you clarify your examples?

scientificName=×Agropogon littoralis (Sm.) C. E. Hubb. (1946)
genus=
species=
infraspecificEpithet=
rank=
nothoTaxon=

Wouldn't a taxonRank=nothospecies be sufficient?

Mar 23, 2012 comment #2 wixner
Peter, it goes like this:

scientificName=×Agropogon littoralis (Sm.) C. E. Hubb. (1946)
genus=Agropogon
species=littoralis
infraspecificEpithet=
scientificNameAuthorship=(Sm.) C. E. Hubb. (1946)
taxonRank=species
nothoTaxon=generic

The trouble here is that the genus is considered to be a hybrid already, but the rank of the taxon still is a species. If it would be a nothospecies it would be Agropogon ×littorals. Im not 100% sure if I interpreted the ICBN correctly, but it seemed to be the use of notho as a prefix to rank terms is limited to infraspecific ranks, e.g. nothosubsp.

Oct 3, 2013 comment #6 gtuco.btuco
I would like to promote the adoption of the concept mentioned in this issue. To do so, I will need a stronger proposal demonstrating the need to share this information - that is, that independent groups, organizations, projects have the same need and can reach a consensus proposal about how the term should be used. It might be a good idea to circulate the proposal on tdwg-content and see if a community can be built around and support the addition.

The TDWF executive has decided to choose for CC BY 4.0 as the default license for all TDWG documents. The attribution requirements are:

1. If You Share the Licensed Material (including in modified
          form), You must:

            a. retain the following if it is supplied by the Licensor
               with the Licensed Material:

                 i. identification of the creator(s) of the Licensed
                    Material and any others designated to receive
                    attribution, in any reasonable manner requested by
                    the Licensor (including by pseudonym if
                    designated);

                ii. a copyright notice;

               iii. a notice that refers to this Public License;

                iv. a notice that refers to the disclaimer of
                    warranties;

                 v. a URI or hyperlink to the Licensed Material to the
                    extent reasonably practicable;

            b. indicate if You modified the Licensed Material and
               retain an indication of any previous modifications; and

            c. indicate the Licensed Material is licensed under this
               Public License, and include the text of, or the URI or
               hyperlink to, this Public License.

       2. You may satisfy the conditions in Section 3(a)(1) in any
          reasonable manner based on the medium, means, and context in
          which You Share the Licensed Material. For example, it may be
          reasonable to satisfy the conditions by providing a URI or
          hyperlink to a resource that includes the required
          information.

       3. If requested by the Licensor, You must remove any of the
          information required by Section 3(a)(1)(A) to the extent
          reasonably practicable.

       4. If You Share Adapted Material You produce, the Adapter's
          License You apply must not prevent recipients of the Adapted
          Material from complying with this Public License.

Tasks

1. To help users, it would be best to provide a document that includes the required information, so people can reference that. I would be best if that information lives at http://rs.tdwg.org/dwc/ and people can just reference that (which is done in numerous applied uses of the standard, e.g. DwC archives).
2. We need to indicate that a URL often suffices. I currently wrote it as:

License

Darwin Core (c) by the Darwin Core Task Group, Biodiversity Informatics Standards (TDWG). Darwin Core is licensed under a Creative Commons Attribution 4.0 International License. A copy of the license is provided in LICENSE.

How to attribute and cite Darwin Core

Use the recommended citation format where possible in publications. For applied uses, referencing http://rs.tdwg.org/dwc/ suffices. The recommended citation format is (substitute the parenthetical date accessed with today's date):

Darwin Core Task Group, Biodiversity Information Standards (TDWG). 2009. Darwin Core. 
http://rs.tdwg.org/dwc/ (accessed on 2014-10-29).

See also #6

This proposal has had extensive commentary and has been updated by @timrobertson100 to accommodate all comments up to Dec 8th 2022. Previous versions of this proposal may be viewed by clicking the "edited" link above, and were the subject of the earlier comments below

New term

• Submitter: Tommy McElrath @tmcelrath, Debbie Paul @debpaul, Tim Robertson @timrobertson100, Christian Bölling @cboelling
• Efficacy Justification (why is this term necessary?): To provide a digital representation derived from and as close as possible in content to what is on the original label(s), in order to provide quality control and comparison to any and all parsed data from a label. Other use cases are outlined here: https://doi.org/10.1093/database/baz129
• Demand Justification (name at least two organizations that independently need this term): Survey of digitizing collections conducted by @tmcelrath (see comments below), DataShot (MCZ), TaxonWorks, GBIF
• Stability Justification (what concerns are there that this might affect existing implementations?): New term, does not adversely affect any existing terms or implementations.
• Implications for dwciri: namespace (does this change affect a dwciri term version)?: As a "verbatim" term, dwc:verbatimLabel is not expected to have a dwciri: analog, so there are no implications in that namespace.

Proposed attributes of the new term:

• Term name (in lowerCamelCase for properties, UpperCamelCase for classes): verbatimLabel

• Organized in Class (e.g., Occurrence, Event, Location, Taxon): MaterialSample

• Definition of the term (normative): A serialized encoding intended to represent the literal, i.e., character by character, textual content of a label affixed on, near, or explicitly associated with a material entity, free from interpretation, translation, or transliteration.

• Usage comments (recommendations regarding content, etc., not normative): The content of this term should include no embellishments, prefixes, headers or other additions made to the text. Abbreviations must not be expanded and supposed misspellings must not be corrected. Lines or breakpoints between blocks of text that could be verified by seeing the original labels or images of them may be used. Examples of material entities include preserved specimens, fossil specimens, and material samples. Best practice is to use UTF-8 for all characters. Best practice is to add comment “verbatimLabel derived from human transcription” in occurrenceRemarks.

• Examples (not normative):

  1. For a label affixed to a pinned insect specimen, the verbatimLabel would contain:

     ILL: Union Co.
     Wolf Lake by Powder Plant
     Bridge. 1 March 1975
     Coll. S. Ketzler, S. Herbert

     Monotoma
     longicollis 4 ♂
     Det TC McElrath 2018

     INHS
     Insect Collection
     456782

     With comment "verbatimLabel derived from human transcription" added in occurrenceRemarks.

  2. When using Optical Character Recognition (OCR) techniques against an herbarium sheet, the verbatimLabel would contain:

     0 1 2 3 4 5 6 7 8 9 10
     cm copyright reserved
     The New York
     Botanical Garden

     NEW YORK
     BOTANICAL
     GARDEN

     NEW YORK BOTANICAL GARDEN
     ACADEMY OF NATURAL SCIENCES OF PHILADELPHIA
     EXPLORATION OF BERMUDA
     NO. 355
     Cymbalaria Cymbalaria (L.) Wettst
     Roadside wall, The Crawl.
     STEWARDSON BROWN
     }COLLECTORS AUG. 31-SEPT. 20, 1905
     N.L. BRITTON

     NEW YORK BOTANICAL GARDEN
     00499439

     With comment “verbatimLabel derived from unadulterated OCR output” added in occurrenceRemarks.

• Refines (identifier of the broader term this term refines; normative): None

• Replaces (identifier of the existing term that would be deprecated and replaced by this term; normative): None. Does not replace any current DWC “verbatim” terms. Other “verbatim” terms have already been “parsed” to a certain data class and have their own uses

• ABCD 2.06 (XPATH of the equivalent term in ABCD or EFG; not normative): /Marks/Mark/MarkText

New Term

Submitter: Markus Döring
Justification: cultivar names can only be shared now via the full scientificName and need their own atomized term.
Proponents: Workshop on Biodiversity Data Quality (2016-03), TCS
Definition: Part of the name of a cultivar, cultivar group or grex that follows the scientific name.
Comment: According to the Rules of the Cultivated Plant Code, a cultivar name consists of a botanical name followed by a cultivar epithet. The value given as the cultivarEpithet should exclude any quotes. The term taxonRank should be used to indicate which type of cultivated plant name (e.g. cultivar, cultivar group, grex) is concerned. This epithet, including any enclosing apostrophes or suffix, should be provided in scientificName as well.
Examples: King Edward (for scientificName "Solanum tuberosum 'King Edward'" and taxonRank "cultivar"); Mishmiense (for scientificName "Rhododendron boothii Mishmiense Group" and taxonRank "cultivar group"); Atlantis (for scientificName "Paphiopedilum Atlantis grex" and taxonRank "grex").
Refines: None
Replaces: None
ABCD 2.06: http://rs.tdwg.org/abcd/terms/cultivarName or http://rs.tdwg.org/abcd/terms/cultivarGroupName or http://rs.tdwg.org/abcd/terms/breed (ABCD 3.0)

Original comment: https://code.google.com/p/darwincore/issues/detail?id=141

Mar 1, 2012 comment #1 dag.endresen
One potential challenge of adding cultivar name as part of the nomenclature code is perhaps that cultivar names can have language. The very same cultivar can be released under different marketing names in different countries.

Mar 2, 2012 comment #2 wixner
isn't that a kind of synonym then? Several names referring to the same taxon. Or does the cultivar code explicitly accept several localisations for one name?

Mar 2, 2012 comment #3 wixner
There is also the need to share information about other informal name parts not governed by the nomenclatoral codes. For example bacterial strain names or temporary names in use before they have been published. Hyloxalus sp. JCS-2010a for example was updated to Hyloxalus yasuni when Paez-Vacas et al. (2010) was published. Other examples are Clostridium botulinum A112 or Clostridium botulinum A strain ATCC 19397.

Is it maybe worthwhile having an informalEpithet instead that caters for both cultivars and temporary names?

Mar 2, 2012 comment #4 dag.endresen
I believe that each 'localization' of a cultivar name could perhaps be seen as the 'valid' name in the country where the name is used/marketed - and as a 'synonym' in other countries...? I am not sure if it is always easy to pick one globally 'valid' cultivar name...? And each cultivar can have different release year in different countries, and I believe sometimes (but not always?) released and marketed under a different cultivar name...?

Mar 2, 2012 comment #5 dag.endresen
The International Code of Nomenclature for Cultivated Plants (ICNCP, Cultivated Plant Code) seems to regulate the 'cultivar epithet' to be a distinct name within a genus - and that the cultivar name (cultivar epithet) is a different thing from the 'trade name', and that it is the 'trade name' that can be a different name for the same cultivar marketed in each country... sorry for the confusion.
http://en.wikipedia.org/wiki/International_Code_of_Nomenclature_for_Cultivated_Plants

Mar 2, 2012 comment #6 dag.endresen
Which could mean that there is a role in Darwin Core for both a new cultivarEpithet and an informalEpithet term...?

Mar 2, 2012 comment #7 wixner
Wikipedia suggests there is only a single cultivar epithet:
http://en.wikipedia.org/wiki/Cultivar#Cultivar_names

"A cultivar name consists of a botanical name (of a genus, species, infraspecific taxon, interspecific hybrid or intergeneric hybrid) followed by a cultivar epithet. The cultivar epithet is capitalised and enclosed by single quotes; it should not be italicized. It is permissible to place a cultivar epithet after a common name provided the common name is botanically unambiguous. Cultivar epithets published before 1 January 1959 were often given a Latin form and can be readily confused with the specific epithets in botanical names; after that date, newly coined cultivar epithets must be in a modern vernacular language to distinguish them from botanical epithets."

A cultivar name also has to be published just like a scientific name before it can be registered. So the publishedIn(Year) terms would also apply nicely.
An example registration page for aroids can be found here:
http://www.aroid.org/cultivars/reg_form_short.php

Mar 2, 2012 comment #8 dag.endresen
There seems to be two systems for cultivar names - one system of "cultivar epithet" under the ICNCP (distinct names published in a journal) - and another system of "trade designations"/"trade names" generally under the UPOV (but with varying national legislation) where different "trade name" can be protected in distinct countries (different years) for the same cultivar. I believe that both these types of "cultivar names" might perhaps be useful to track...?

"Many plants have "selling names" or "marketing names" as well as a cultivar name; the ICNCP refers to these as "trade designations". Only the cultivar name is governed by the ICNCP. It is required to be unique", http://en.wikipedia.org/wiki/International_Code_of_Nomenclature_for_Cultivated_Plants.

Mar 6, 2012 comment #9 wixner
Added a new issue144 for strains

Sep 23, 2013 comment #12 gtuco.btuco
I would like to promote the adoption of the concepts mentioned in this issue. To do so, I will need a stronger proposal demonstrating the need to share this information - that is, that independent groups, organizations, projects have the same need and can reach a consensus proposal about how the term or terms should be used. It might be a good idea to circulate the proposal on tdwg-content and see if a community can be built around and support the additions.

New Term Recommendation

Submitter: Markus Döring
Justification: In order to accurately represent the genus part of a parsed scientific name a new term is needed as dwc:genus is (for good reasons) defined to be the accepted genus, see discussion in https://code.google.com/p/darwincore/issues/detail?id=151
Proponents: GBIF, Catalogue of Life
Definition: The genus part of the scientificName without authorship.
Comment: For synonyms the accepted genus and the genus part of the name may be different. The term genericName should be used together with specificEpithet to form a binomial and with infraspecificEpithet to form a trinomial. The term genericName should only be used for combinations. Uninomials of generic rank do not have a genericName.
Examples: Felis (for scientificName "Felis concolor", with accompanying values of "Puma concolor" in acceptedNameUsage and "Puma" in genus).
Refines: None
Replaces: None
ABCD 2.06: https://abcd.tdwg.org/terms/#genusOrMonomial (ABCD 3.0)

Original comment:

Was https://code.google.com/p/darwincore/issues/detail?id=227

==New Term Recommendation==
Submitter: Markus Döring

Justification: In order to accurately represent the genus part of a parsed scientific name a new term is needed as dwc:genus is (for good reasons) defined to be the accepted genus, see discussion in https://code.google.com/p/darwincore/issues/detail?id=151

Definition: The genus part of the scientificName without authorship

Comment: For synonyms the accepted genus and the genus part of the name are different. For example for "Felis concolor" dwc:genus is Puma while dwc:genericName is Felis.

Refines:

Has Domain:

Has Range:

Replaces:

ABCD 2.06:

Feb 14 2014 Comment #1 wixner
This proposed new term is already in use by GBIF and the Catalog of Life (i4Life Darwin Core Archive Profile)

Mar 27, 2014 comment #3 [email protected]
Why would this term not be called genericEpithet, like all the other name parsed terms - specificEpithet, infraspecificEpithet, cultivarEpithet? In this context, it is just another epithet in the name. Why not be consistent? It is the "genus part of the name" but calling it "genericName" allows other interpetations? Epithet is what we have been using to refer to "part of a name".

Mar 27, 2014 comment #4 wixner
Could do, Chuck. My understanding of epithet though is a word that is "attached" to some existing thing. A refinement if you like. And the genus is the main part which the epithet refines, therefore I did not think genericEpithet is applicable. But this might simply be me not being a native english speaker. Wikipedia seems to support that view though: http://en.wikipedia.org/wiki/Epithet

In the TDWG ontology it is called "genusPart": http://rs.tdwg.org/ontology/voc/TaxonName.rdf#genusPart
In TCS simply Genus

Jul 25, 2014 comment #5 morris.bob
Speaking as a non-biologist, I'd really like to see both biological and informatics arguments about the point raised in #1, #3 and #4.
On one hand, #1 shows there are important use cases. On the other hand, the consistency advocated in #3 seems appealing, but I have no opinion on the linguistics discussion in #3 and #4, especially as use of DwC in general may find one or the other of arguably better.

In general, I believe that a use of unratified terminology in a particular case---here the i4Life profile and perhaps others(?)---should be viewed with suspicion if it does not generalize to other cases that the community needs to support. Alas, I have no way to judge if that is so here.

Was https://code.google.com/p/darwincore/issues/detail?id=190

==New Term Recommendation==

Submitter: John Wieczorek on behalf of the May 2013 GBIF hackathon-workshop on Darwin Core and sample data

Justification: see "Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)" at http://www.gbif.org/orc/?doc_id=5424

Term Name: environmental feature
Identifier: http://purl.obolibrary.org/obo/ENVO_00002297
Namespace: http://purl.obolibrary.org/obo/
Label: Environmental Feature
Definition: A prominent or distinctive aspect, quality, or characteristic of a biome.
Comment: Examples: "meadow", "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see https://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified)
Type of Term: http://www.w3.org/2000/01/rdf-schema#Class
Refines:
Status: proposed
Date Issued: 2013-09-25
Date Modified: 2013-09-25
Has Domain:
Has Range:
Refines:
Version: http://purl.obolibrary.org/obo/ENVO_00002297
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

Note that the current official definition for this term is "A feature that is." I sent a request to [email protected] to change the definition to be the same as what I put in the proposal above.

Sep 26, 2013 comment #1 gtuco.btuco
Based on initial discussions on tdwg-content, modified the proposal to make a new DwC property term that recommends the ENVO class as the range, as follows:

Term Name: environmentalFeature
Identifier: http://rs.tdwg.org/dwc/terms/environmentalFeature
Namespace: http://rs.tdwg.org/dwc/terms/
Label: Environmental Feature
Definition: A prominent or distinctive aspect, quality, or characteristic of a biome. Recommended best practice is to use a controlled vocabulary such as defined by the environmental feature class of the Environment Ontology (ENVO).
Comment: Examples: "meadow", "http://purl.obolibrary.org/obo/ENVO_00000108". For discussion see https://code.google.com/p/darwincore/wiki/Event (there will be no further documentation here until the term is ratified)
Type of Term: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
Refines:
Status: proposed
Date Issued: 2013-09-26
Date Modified: 2013-09-26
Has Domain:
Has Range:
Refines:
Version: environmentalFeature-2013-09-26
Replaces:
IsReplaceBy:
Class: http://rs.tdwg.org/dwc/terms/Event
ABCD 2.0.6: not in ABCD (someone please confirm or deny this)

DOIs are already automatically assigned, but it might be good to:

• Add those DOIs to the releases on GitHub
• Add more metadata (e.g. authors) to the packages on Zenodo.
• 2021-08-24: https://doi.org/10.5281/zenodo.5251698 part of DOI version chain 1
• 2020-08-20: https://doi.org/10.5281/zenodo.5136636 part of DOI version chain 1
• 2014-11-08: https://doi.org/10.5281/zenodo.12694 part of DOI version chain 1
• 2013-10-23: https://doi.org/10.5281/zenodo.12693 part of DOI version chain 2
• 2011-10-26: https://doi.org/10.5281/zenodo.12691 part of DOI version chain 1
• 2009-12-07: https://doi.org/10.5281/zenodo.5593192 part of DOI version chain 3
• 2009-10-08: https://doi.org/10.5281/zenodo.5593189 part of DOI version chain 3
• Remove pre-releases from Zenodo
• Correct authors for https://doi.org/10.5281/zenodo.12691

See some examples at:

https://code.google.com/p/tdwg-rdf/wiki/DwcRdfOccurrences

Where should these live? All on the README.md, or in the Wiki? If the former, we will need a good Table of Contents.