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Darwin Core guidelines for herbaria
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).
Original issue reported on code.google.com by [email protected]
on 25 Sep 2011 at 4:25
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.
Original issue reported on code.google.com by [email protected]
on 2 Feb 2012 at 7:45
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.
Original issue reported on code.google.com by [email protected]
on 26 Mar 2012 at 1:16
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- sex
- lifeStage
- reproductiveCondition
- behavior
- establishmentMeans
- occurrenceStatus
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:02
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)
Original issue reported on code.google.com by [email protected]
on 9 Jun 2011 at 4:35
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- individualID
- individualCount
This includes the discussion about multiple sheets, preparations and what a
specimen is.
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:01
A question from Amber Saundry at UBC:
For the DwC term scientificNameAuthorship โ 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
Original issue reported on code.google.com by [email protected]
on 9 Feb 2012 at 12:02
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- identifiedBy
- dateIdentified
- identificationQualifier
- identificationRemarks
- identificationReferences
- previousIdentifications
This includes the discussion about simple vs. star-schema Darwin Core.
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:08
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Write guidelines for:
- samplingProtocol
- samplingEffort
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:03
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Write guidelines for:
- preparations
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:02
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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
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 8:17
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- minimumElevationInMeters
- maximumElevationInMeters
- verbatimElevation
- minimumDepthInMeters
- maximumDepthInMeters
- verbatimDepth
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:05
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- eventDate
- eventTime
- startDayOfYear
- endDayOfYear
- year
- month
- day
- verbatimEventDate
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:03
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.
Original issue reported on code.google.com by [email protected]
on 9 Jun 2011 at 8:34
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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?
Original issue reported on code.google.com by [email protected]
on 9 Feb 2012 at 9:27
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- habitat
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:03
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else, please change the template above.)
Please describe what needs to be done. Include links if possible.
Write documentation for:
- scientificName
- genus
- subgenus
- specificEpithet
- infraspecificEpithet
- scientificNameAuthorship
- taxonRank
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:09
[deleted issue]
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- dynamicProperties
- associatedMedia
- associatedReferences
- associatedOccurrences
- associatedSequences
- associatedTaxa
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:00
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Please describe what needs to be reviewed. Include links if possible.
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.
Original issue reported on code.google.com by [email protected]
on 13 Jun 2011 at 8:32
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Please describe what needs to be done. Include links if possible.
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
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 8:22
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.
Original issue reported on code.google.com by [email protected]
on 12 Nov 2011 at 8:19
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- recordedBy
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:00
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!
Original issue reported on code.google.com by [email protected]
on 10 Jun 2011 at 4:32
[deleted issue]
Some changes in Darwin Core were ratified at TDWG. We need to update our files.
Original issue reported on code.google.com by [email protected]
on 17 Nov 2011 at 4:15
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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.
Original issue reported on code.google.com by [email protected]
on 30 Aug 2011 at 3:20
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.
Original issue reported on code.google.com by [email protected]
on 11 Jul 2013 at 3:15
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- higherGeographyID
- higherGeography
- continent
- islandGroup
- island
- country
- countryCode
- stateProvince
- county
- municipality
- locality
- verbatimLocality
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:04
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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?
Original issue reported on code.google.com by [email protected]
on 9 Jun 2011 at 3:02
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"/>
Original issue reported on code.google.com by [email protected]
on 9 Jun 2011 at 5:19
ListOfTerms has a column headed "Term URL". "URL" is a loaded term, and I hope
this is intended to be "Term URI."
Original issue reported on code.google.com by morris.bob
on 21 Feb 2012 at 5:28
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:
Original issue reported on code.google.com by [email protected]
on 11 Jun 2011 at 4:06
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Please describe what needs to be done. Include links if possible.
Write the guidelines for:
- informationWithheld
- dataGeneralizations
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 9:57
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Write guidelines for:
- decimalLatitude
- decimalLongitude
- geodeticDatum
- coordinateUncertaintyInMeters
- coordinatePrecision
- verbatimLatitude
- verbatimLongitude
- verbatimCoordinates
- verbatimCoordinateSystem
- verbatimSRS
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:07
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Write guidelines for:
- decimalLatitude
- decimalLongitude
- geodeticDatum
- coordinateUncertaintyInMeters
- coordinatePrecision
- georeferenceSources
- georeferencedBy
- georeferenceProtocol
- georeferenceSources
- georeferenceVerificationStatus
- georeferenceRemarks
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:06
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Write the guidelines for:
- dcterms:rights
- dcterms:rightsHolder
- ownerInstitutionCode
- dcterms:accessRights
- dcterms:bibliographicCitation
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 9:58
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
Original issue reported on code.google.com by [email protected]
on 20 Jul 2011 at 7:02
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...
Original issue reported on code.google.com by morris.bob
on 10 Oct 2011 at 5:12
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- ownerInstitutionCode
- institutionID
- institutionCode
- collectionID
- collectionCode
- datasetID
- datasetName
- catalogNumber
- otherCatalogNumbers
- recordNumber
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:11
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Write guidelines for:
- typeStatus
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:08
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Please describe what needs to be done. Include links if possible.
Write guidelines for:
- higherClassification
- kingdom
- phylum
- class
- order
- family
- genus
- subgenus
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 10:09
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Please describe what needs to be done. Include links if possible.
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)
Original issue reported on code.google.com by [email protected]
on 9 Jun 2011 at 4:36
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else, please change the template above.)
Please describe what needs to be reviewed. Include links if possible.
I've just written the recommendations for codes and numbers attached to a
specimen. Please review: http://code.google.com/p/applecore/wiki/CodesAndNumbers
Original issue reported on code.google.com by [email protected]
on 7 Jun 2011 at 9:55
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
Original issue reported on code.google.com by [email protected]
on 2 Feb 2012 at 8:11
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