xjsachs / applecore Goto Github PK

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Write guidelines for:
- ownerInstitutionCode
- institutionID
- institutionCode
- collectionID
- collectionCode
- datasetID
- datasetName
- catalogNumber
- otherCatalogNumbers
- recordNumber

Initially we thought that datasetID could not be used, as there is no registry 
for this. But just like for the institutionID, we could use the GBRDS, which 
issues a UUID per dataset (called "resource"), e.g. 
http://gbrds.gbif.org/browse/agent?uuid=ada5d0b1-07de-4dc0-83d4-e312f0fb81cb

1. I think it is a suitable value for datasetID. However, one can only provide 
after the dataset has been published.

2. Should we use the UUID or the full link (see issue 28)

3. Should the ID provided in datasetID apply to the same unit as the name 
provided in datasetName (just like for collectionCode/ID and 
institutionCode/ID). I'm asking because we currently advise to use datasetName 
to indicate the name of the subcollection (if any), which is definitely NOT the 
same unit as the whole dataset.

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Include a clear, all-encompassing and preferably real-life example at the end 
of http://code.google.com/p/applecore/wiki/CodesAndNumbers.

The collection in the example should have:
- An higher institution with an ID
- Subcollections
- A BCI LSID
The specimen in the example should have:
- Other specimen numbers
- A collector number

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Write guidelines for:
- higherGeographyID
- higherGeography
- continent
- islandGroup
- island
- country
- countryCode
- stateProvince
- county
- municipality
- locality
- verbatimLocality

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Write guidelines for:
- recordedBy

ListOfTerms has a column headed "Term URL".  "URL" is a loaded term, and I hope 
this is intended to be "Term URI."

[deleted issue]

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Write guidelines for:
- individualID
- individualCount

This includes the discussion about multiple sheets, preparations and what a 
specimen is.

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Write guidelines for:
- samplingProtocol
- samplingEffort

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Write guidelines for:
- dynamicProperties
- associatedMedia
- associatedReferences
- associatedOccurrences
- associatedSequences
- associatedTaxa

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Write guidelines for:
- higherClassification
- kingdom
- phylum
- class
- order
- family
- genus
- subgenus

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I have finished writing the guidelines for Collection Date. Please review them 
at: http://code.google.com/p/applecore/wiki/CollectionDate

- If you agree with the text, leave a comment here.
- If things are unclear or missing, or you have issues with certain
recommendations, open a discussion about that topic:
http://code.google.com/p/applecore/issues/entry
- If you discover typos, notify me or correct them in the wiki.

I need 3 review confirmations before I can close this issue.

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Write guidelines for:
- habitat

Please describe your question as clearly as possible. Include links if possible.

What are the DwC guidelines related to the handling of hybrid entities without 
a formal hybrid name - e.g. "Crataegus monogyna Jacq. x Crataegus suksdorfi 
(Sarg.) Kruschke".

Are there already rules of thumb for these examples or is this an area were DwC 
is vague or agnostic?  If the latter, perhaps useful to tackle in the 
guidelines.

(Question by Patrick Sweeney)

Some changes in Darwin Core were ratified at TDWG. We need to update our files.

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Write the guidelines for:
- dcterms:rights
- dcterms:rightsHolder
- ownerInstitutionCode
- dcterms:accessRights
- dcterms:bibliographicCitation

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What are the DwC guidelines related to the handling of cultivars names - e.g., 
Crataegus 'Loch Lomond' or Clematis alpina 'Ruby', etc.

Are there already rules of thumb for these examples or is this an area were DwC 
is vague or agnostic?  If the latter, perhaps useful to tackle in the 
guidelines.

(Question by Patrick Sweeney)

On the codes and numbers page of the wiki, 
https://code.google.com/p/applecore/wiki/CodesAndNumbers there is a section on 
SpecimenNumber that describes the use the catalogNumber term.  

The guidance and examples seem to suggest that the catalog number should 
include the Herbarium Acronym, the subcollection or catalog number series if 
such is needed to disambguate numbers within a herbarium, and the actual 
catalog number of the specimen itself.  

The discussion of subcollections, however provides two examples that appear to 
use only the subcollection and the catalog number, and not include the 
herbarium acronym.  

I'd suggest adding annother example to the pair at the bottom of the page which 
includes a subcollection, and clarifying the discussion of subcollections (I'd 
suggest doing so by adding a herbarium acronym to the two examples, BRYO-10001 
and VASC-10001, changing them to MT-BRYO-10001 and  MT-VASC-10001.

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Write guidelines for:
- decimalLatitude
- decimalLongitude
- geodeticDatum
- coordinateUncertaintyInMeters
- coordinatePrecision
- verbatimLatitude
- verbatimLongitude
- verbatimCoordinates
- verbatimCoordinateSystem
- verbatimSRS

We need to decide on the best practices for sharing a collection date in Apple 
Core:
http://rs.tdwg.org/dwc/terms/eventDate
http://rs.tdwg.org/dwc/terms/verbatimEventDate

There are 3 approaches:

== Approach 1 ==

verbatimEventDate = the date as close to the original as possible. This means 
that if no verbatim date is recorded in the database, an altered/structured 
date might be provided in this term.
eventDate = the date formatted according to ISO 8601:2004(E). No other date 
formats are accepted.

Advantage: The collection can always provide a date (in verbatimEventDate).
Disadvantage: The data user has no guarantee the date in verbatimEventDate has 
not been altered/structured (if there is a image of the label available, he 
has).

== Approach 2 ==
verbatimEventDate = the original date as on the label. This means that if no 
verbatim date is recorded in the database, an altered/structured date can NOT 
be provided.
eventDate = the date formatted according to ISO 8601:2004(E). No other date 
formats are accepted.

Advantage: The data user has the guarantee that the date in verbatimEventDate 
has not been altered/structured. It depends of course how you interpret 
altered: is something like "Sum... 199. [illisible]" accepted (which is 
something you might find in a verbatim date field in a collection database)?
Disadvantage: The collection might not be able to provide any date at all: when 
they do not record the verbatim date and are not able to transform the date 
they have to ISO.

== Approach 3 ==
verbatimEventDate = the original date as on the label. This means that if no 
verbatim date is recorded in the database, an altered/structured date can NOT 
be provided.
eventDate = the altered/structured date. Preferably in ISO 8601:2004(E), but 
not mandatory.

Advantage: The collection can always provide a date (in eventDate). The data 
user has the guarantee that the date in verbatimEventDate has not been 
altered/structured (but see remark above).
Disadvantage: the eventDate cannot be readily consumed by aggregators.

A question from Amber Saundry at UBC:
For the DwC term scientificNameAuthorship – this should be the authorship of 
the lowest rank.  However, what about when there is an subspecies/variety/forma 
autonym (ie: Salix brachycarpa Nutt. subsp. brachycarpa)?  Should this field 
reflect the species authorship (Nutt.), or be blank, as the subspecies level 
has no authorship?

What would you suggest? 
http://rs.tdwg.org/dwc/terms/index.htm#scientificNameAuthorship

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The goal of Apple Core is currently a one-sentence in the introduction. This 
should be expanded and put into context: 
http://code.google.com/p/applecore/wiki/Introduction

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Write guidelines for:
- typeStatus

[deleted issue]

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Write guidelines for:
- minimumElevationInMeters
- maximumElevationInMeters
- verbatimElevation
- minimumDepthInMeters
- maximumDepthInMeters
- verbatimDepth

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Write guidelines for:
- eventDate
- eventTime
- startDayOfYear
- endDayOfYear
- year
- month
- day
- verbatimEventDate

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Can someone give an example for the term institutionID 
(http://rs.tdwg.org/dwc/terms/institutionID)?
Are there any registries for institutions who issue identifiers?

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Write documentation for:
- scientificName
- genus
- subgenus
- specificEpithet
- infraspecificEpithet
- scientificNameAuthorship
- taxonRank

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Write guidelines for:
- decimalLatitude
- decimalLongitude
- geodeticDatum
- coordinateUncertaintyInMeters
- coordinatePrecision
- georeferenceSources
- georeferencedBy
- georeferenceProtocol
- georeferenceSources
- georeferenceVerificationStatus
- georeferenceRemarks

Should the CollectionID from the biodiversity collections index use the 
resolvable http://biocol.or/urn:lsid:biocol.org or the raw 
urn:lsid:biocol.org:col form of the identifier? 

The rdf document that biocol delivers for a collection includes an owl:sameAs 
linking the two.  For example in: 
http://biocol.org/collection/rdf/id/15406

<tc:Collection rdf:about="urn:lsid:biocol.org:col:15406">
<owl:sameAs rdf:resource="http://biocol.org/urn:lsid:biocol.org:col:15406"/>

Please describe your question as clearly as possible. Include links if
possible.

I now know two herbaria (MT, TRTE) who are recording in which herbaria 
duplicates/replicates of the specimen can be found. There are probably other 
herbaria doing the same. The field lists the herbarium acronyms concatenated 
and separated:

duplicatesAt: NFLD; UWO; DAO

Questions:

1. Is this useful information to share in Darwin Core? For regular users, 
FilteredPush users?

2. How can we share this in Darwin Core? No term seems appropriate.

The closest one might be 
http://rs.tdwg.org/dwc/terms/index.htm#associatedOccurrences, but that should 
list the IDs for the associated specimens, not the collections where they are 
deposited. Is there a way we can interpret this definition in a broader sense?

The other option is of course 
http://rs.tdwg.org/dwc/terms/index.htm#dynamicProperties. Since the key value 
pairs in this term are generally separated by ";", just dumping duplicatesAt 
(containing ";") will probably cause problems. Are any of these useable?

A. duplicatesAt=NLFD,UWO,DAO; otherDynamicProperty=...

B. duplicateAt=NLFD; duplicateAt=UWO; duplicateAt=DAO; otherDynamicProperty=...

Any advise would be welcome. Based on the feedback here, TRTE will either 
publish or not publish this information before Thursday, March 29th, after 
which it will be difficult to change it.

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Write guidelines for:
- sex
- lifeStage
- reproductiveCondition
- behavior
- establishmentMeans
- occurrenceStatus

Some specimens have multiple dates on their specimen label, for example: one 
for the flowers and one for the plant itself: "May 16 and August 7, 1991". For 
insect specimens I've even seen triple dates.

How do we advise to express such a date in eventDate 
(http://rs.tdwg.org/dwc/terms/index.htm#eventDate)?

1) No eventDate
verbatimEventDate: May 16 and August 7, 1991
eventDate: 
startDayOfYear: 
endDayOfYear:
year: 1991
month: 
day: 

2) Separated dates in eventDate:
verbatimEventDate: May 16 and August 7, 1991
eventDate: 1991-05-16|1991-08-07
startDayOfYear: 
endDayOfYear:
year: 1991
month: 
day: 

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Write the guidelines for:
- informationWithheld
- dataGeneralizations

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Write guidelines for:
- preparations

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Please describe what needs to be done. Include links if possible.
http://code.google.com/p/applecore/wiki/CodesAndNumbers

institutionID is mentioned in the list, but there is no recommendation.

We need a policy for terms we recommend not to use.

The Project Home carries the text
"Apple Core datasets will be expressible as Simple Darwin Core or as an 
Occurrence core (http://rs.gbif.org/core/dwc_occurrence.xml) with an 
Identification History extension 
(http://rs.gbif.org/extension/dwc/identification.xml)."

Since "Simple Darwin Core" is an organizing principle, not a constraint set, is 
the meaning of the first clause "will be expressible in a way  that conforms to 
http://rs.tdwg.org/dwc/terms/simple/index.htm" or does it mean "will be 
expressible in a way that conforms to either 
http://rs.tdwg.org/dwc/xsd/tdwg_dwc_simple.xsd or 
http://rs.tdwg.org/dwc/examples/text/example_text_simpledwc_complete.xml"

If the latter (which I hope is the case), it would be wise to specify a version 
of each of those, or at least urge that serializations carry enough information 
to know which.

If you mean the organizing principle thingie, you may open an unknown future 
can of worms...

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I've just written the recommendations for codes and numbers attached to a 
specimen. Please review: http://code.google.com/p/applecore/wiki/CodesAndNumbers

Hello,

I recently posted a question on the DwC wiki about validating DwC dates. I am 
very pleased to see that my question received prompt attention. I now have a 
few questions about implementation, and hope this is the right venue for them. 
If not, I would be happy to hear of a better place if anyone can point me in 
the right direction.

As I see it, Simple DwC does not allow the reuse of fields within a record, nor 
modifications to the fields themselves. I am not sure how to handle some of the 
data in our herbarium data with these limitations. The field "vernacularName" 
is one such problem. Our current data contains the common names for plants in 
English and French. In some cases there are also Aboriginal names as well 
(though only in the print catalogue at this point). It would be helpful for use 
if we could use <DwC:vernacularName lang=en> or something similar so that we 
may keep the data complete, yet differentiate between the  vernacular names. We 
have a similar problem (as I see it) with verbatimLatitude and related terms. 
Our data includes both Lat/Long data (sometimes in decimal form, sometimes 
verbatim deg., min., sec.) and also UTM data. It seems to me that we should not 
favour one over the other, but keep both - especially since I don't know the 
origins of the location data (our herbarium samples have been collected by many 
different people over the last 200 years so there is little consistency).

I am creating a mapping to transfer our data to DwC. The (working) document in 
MS Excel can be found <a 
href=http://dl.dropbox.com/u/23721205/HerbariumDB/HerbDBMappingCleanedUp.xlsx>he
re</a>. There's still lots to be done in the Taxon area. I am a librarian, not 
a biologist, and the data is all new to me. I am getting some help from the 
good people at the herbarium, but am quite open to any other help or 
suggestions.

Many thanks,
Geoffrey

The HUH botanist list includes two terms for missing values for botanists (when 
used as collectors or other agents).  

[no data available]
http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/edd03166-1ec7-45d7-9f7d-d5bd7
4e3e789

[illegible]  
http://purl.oclc.org/net/edu.harvard.huh/guid/uuid/eab40a35-3bd3-4699-a1bc-cb247
439e44b

The Macrofungal TCN has proposed the value: 
[collector unspecified] to use in cases where no collector was specified on the 
collector label. 

AppleCore should provide guidance on what values to use under what conditions.  

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According to Darwin Core definition, the scientificName term is:
The full scientific name, with authorship and date information if known. When 
forming part of an Identification, this should be the name in lowest level 
taxonomic rank that can be determined.
http://rs.tdwg.org/dwc/terms/index.htm#scientificName

Thus, if you have the authorship in your database, you should include in the 
scientificName field. In practice though, I see a lot of people (including 
myself) populate the field without the authors. I asked Laura Russell from 
VertNet (zoology), and that seems very common there too. It is also included as 
an example in for the term: Ambystoma tigrinum diaboli" (genus + 
specificEpithet + infraspecificEpithet)

I remember there was a TDWG discussion about this (will try to find the link at 
some point), but I am now wondering if I should change our dataset, and more 
importantly what I should suggest to my community. John, what do you suggest to 
VertNet members? Are they ignoring your advise?

The discussion in Issue 19 
(http://code.google.com/p/applecore/issues/detail?id=29) makes me realize that 
we'll have many cases where "what data users would like" and "what data 
publishers can provide" are very different. The Apple Core guidelines do have 
to cater to the lowest common denominator, so everyone can publish data.

But I'm thinking that it might be useful (and fun!) to have one or more 
"standards of excellence" or "certificates" for published data. For example: my 
data is published according to APPLE CORE GOLD!

The "Apple Core Gold" standard would be assigned only to data that were 
published following the most strict guidelines in Apple Core, for example 
eventDates are formatted according to ISO 8601:2004(E). I've created a page 
where we can list the conditions for this standard at: 
http://code.google.com/p/applecore/wiki/AppleCoreGold

That way, we don't alienate collections who cannot follow the most strict 
guidelines AND there's an incentive for publishers who can, improving the 
overall quality and usefulness of the data.

To keep things simple, I'm also thinking the following:

1) The standard is be self-assigned: in the open sharing environment of the web 
it is rather easy to debunk it (followed by eternal shame for the publisher, 
unless they step things up). We could also do it peer reviewed or done by a 
trusted registry, but that's a bit too complicated. 

2) You need to comply with ALL the conditions of Apple Core Gold to obtain it. 
That way it can be referenced: a URL to the Apple Core Gold page informs the 
data user what he/she can expect. An Apple Core Gold 88% seems to complicated.

Things I haven't figured out yet (this idea is still rather new):

1) Where in the metadata (DarwinCore or EML) do we record this? Preferably we 
record the URL of the Apple Core Page. If we need to create a new field, it's 
similar in function to georeferenceProtocol.

2) Do we need Apple Core Silver, Apple Core Bronze, Apple Core and maybe an 
Apple Core Rotten?

Let me know what you think!

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Write guidelines for:
- identifiedBy
- dateIdentified
- identificationQualifier
- identificationRemarks
- identificationReferences
- previousIdentifications

This includes the discussion about simple vs. star-schema Darwin Core.

The iDigBio request for comments on a GUID policy 
https://www.idigbio.org/content/globally-unique-identifiers-guid  raises the 
issue of what the GUIDs in various TDWG DarwinCore terms are intended to 
reference.  We should provide guidance on the use of the occurranceID and 
dcterms:references terms.  

We should probably amplify the DarwinCore statement about occurranceID being an 
identifier of the underlying thing (and clarify if we expect this to be a 
herbarium sheet or a duplicate set) rather than it's digital representation.

I'll suggest we should support and amplify the DarwinCore suggestion of using 
the scheme urn:catalog:[institutionCode]:[collectionCode]:[catalogNumber] for 
occurranceID when a GUID is not available.

We could also suggest use of dcterms:references as a pointer to a canonical 
digital representation of the occurrance.  This appears to be what is done in 
the DarwinCore examples of 
references=http://mvzarctos.berkeley.edu/guid/MVZ:Mamm:165861  and 
occurranceID=urn:catalog:FMNH:Mammal:145732

Are we interpreting this too broadly?

According to DwC this term is for expressing _doubt_ about a particular 
determination, so if we keep with this strict definition, our terms sensu 
stricto, sensu lato, etc. are not appropriate.

Regardless of how broadly interpret identificationQualifier, I think we leave 
nomenclatural terms out (e.g., nomen nudum).