New subject: A plea around basisOfRecord

15 Oct 2013

      There is a lot of content here, but let me try to address a few topics.
...
From Donald's original email:
...
2.       basisOfRecord values should be taken from a hierarchical
vocabulary with three main branches:
a.       ?specimens? (i.e. biological material that can be
reviewed), with a hierarchy of subordinate values such as
?pinnedSpecimen?, ?herbariumSheet?, etc.
b.      derived, non-biological evidence (not sure what name),
with a hierarchy of subordinate values such as ?dnaSequence?,
?soundRecording?, ?stillImage?, etc.
c.       asserted observations with no revisitable evidence other
than the authority of the observer

I agree with the idea of having basis of record organized as a hierarchical
vocabulary (preferably as an ontology), but disagree with the proposed
hierarchy, mostly because b groups fundamentally different types of
entities. The BCO is working on just such a hierarchy, and could easily
include any terms needed for basis of record. If the exact subclassOf
hierarchy of the BCO is not ideal for Darwin Core, syntactic classes that
group terms based on other criteria can be used for DwC.
...
...
3.       TDWG should deliver a basic ontology in the form of a
graph of key relationships between the most significant
conceptual entities in our world (TaxonName, TaxonConcept,
Identification, Collection, Specimen, Locality, Agent, ?)

The BCO could serve as this basic ontology for TDWG. Some additional
classes would be needed, and maybe those could come from the TDWG ontology
(but I would need to look into that). The BCO is intended to serve a
broader need than just linking Darwin Core archives, but it is a simple
matter to make a subset that would serve the specific needs of TDWG. The
advantage of using BCO is that it is designed to be compatible with other
kinds of life science ontologies and data, which makes it more flexible and
more likely that it will fulfill unforseen future needs. I (along with
co-authors) plan to give some more background on this approach in a talk at
TDWG in a few weeks. I am not ruling out DSW as a potential solution,
either. My main concerns with DSW are 1) it is tightly coupled to the
Darwin Core and therefor inherits some of the limitations of the Darwin
Core. 2) many of the classes and relations are application specific, and
therefor not interpretable outside the context of the application. I am
looking forward to learning more about DSW at the upcoming TDWG meeting,
where I expect there will be lengthy discussions of the relative merits of
DSW versus BCO. Both ontologies will be presented in the same session.
...
...
4.       This ontology should not attempt to map all the
complexity of biodiversity-related data ? just provide the
high-level map and key relationships (TaxonConcept hasName
TaxonName, Specimen heldIn Collection, etc.) ? it should leave
definition of other properties as a separate, open-ended activity
for the community

The BCO is more of an open-ended activity that attempts to model of
biodiversity, but, as I mentioned above, subsets can be created for more
specific needs. In contrast, creating small, application-specific
ontologies for every application does little to overcome the problem of
data silos. When everyone makes their own ontology, we are not any better
off than when there are no ontologies.
...
...
5.       This ontology should be reviewed at regular intervals
and versioned as necessary to address critical gaps ? provided
that backwards compatibility is maintained (splitting a class
into multiple consitituent classes probably won?t break anything,
so start simple)

An essential part of any ontology is maintenance.
...
...
7.       Every Darwin Core term should be documented to be
tightly associated with a single, fixed class in the ontology
(e.g. scientificName and specificEpithet are ALWAYS considered to
be properties of a TaxonName whether or not that TaxonName object
is clearly referenced or separated out)

What I see as one of the fundamental problems with DwC is that the bulk of
the terms are properties. That means that when data suppliers enter data in
a spread sheet, they are entering literals or URIs that are the objects of
these properties. Having hundreds of properties that are unique to DwC
seriously limits the interoperability of DwC tagged data sets (as I
mentioned in response to point 4). I think a better solution would be to
create ontology classes for most of the DwC terms (along with a few
properties), and then create data annotations that are instances of those
classes. That is a much more common way of organizing ontology-annotated
data and would allow reasoners to work over the data. However, this would
be a fundamental change to the nature of the Darwin Core.
...
...
8.       Every data publisher should be encouraged to share all
relevant data elements in their source data in the most
convenient normalised or denormalised form, provided they use the
recognised Darwin Core properties for elements that match the
definition for those terms, and provided they give some metadata
for other elements.  Possible forms include:
a.       A completely hierarchical, ABCD-like, XML representation
b.      A completely flat denormalised, simple-DwC-like, CVS
representation, if the data includes no elements with higher
cardinality
c.       A set of flat, relational, CVS representations, as with
Darwin Core Archive star schemas, but with freedom to have more
complex graphed relationships as needed

It is important to limit the set of acceptable formats, and develop tools
for interconversion among those formats.
...
...
9.       Each table of CVS data in 8b and 8c is a view that
corresponds to a linear subgraph of the TDWG ontology, identified
by the classes of the DwC properties used ? this allows us to
infer the ?shape? of the data in terms of the ontology

If all DwC terms were classes or properties (depending on which was more
relevant) in an ontology, the graph could be inferred automatically. There
are already tools for converting tabular ontology-tagged data into an
ontology graph.
Ramona
------------------------------------------------------
Ramona L. Walls, Ph.D.
Scientific Analyst, The iPlant Collaborative, University of Arizona
Laboratory Research Associate, New York Botanical Garden
On Mon, Oct 14, 2013 at 3:00 AM, tdwg-content-request@lists.tdwg.orgwrote:
...
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Today's Topics:

Re: A plea around basisOfRecord (Was: Proposed new Darwin
Core terms - abundance, abundanceAsPercent) (Steve Baskauf)
Re: A plea around basisOfRecord (Was: Proposed    new Darwin
Core terms - abundance, abundanceAsPercent) (Steve Baskauf)

Message: 1
Date: Sun, 13 Oct 2013 17:13:58 -0500
From: Steve Baskauf steve.baskauf@vanderbilt.edu
Subject: Re: [tdwg-content] A plea around basisOfRecord (Was: Proposed
        new Darwin Core terms - abundance, abundanceAsPercent)
To: Robert Guralnick Robert.Guralnick@colorado.edu
Cc: TDWG Content Mailing List tdwg-content@lists.tdwg.org
Message-ID: 525B1B26.1010806@vanderbilt.edu
Content-Type: text/plain; charset="windows-1252"
Sorry, I don't agree at all.
The core Darwin-SW classes include only Darwin Core classes and the two
proposed DwC classes (Organism and CollectionObject a.k.a.
dsw:IndividualOrganism and dsw:Evidence) which underwent 30 day public
comment period [1] and were submitted to the Executive which recommended
further consideration by the RDF Task Group and the community at large.
The Documenting Darwin Core sessions at the TDWG meeting will pick up
these and other open issues for further discussion and hopefully move
them towards closure one way or the other.  If the two proposed classes
are at some point accepted for inclusion in DwC, Darwin-SW will use the
new classes and deprecate dsw:IndividualOrganism and dsw:Evidence,
leaving only Darwin Core classes as the core classes in Darwin-SW.
It is NOT my view that Darwin-SW is unable to handle current needs for
linking resources effectively.  If anyone wants to know why I say that,
come to our talk in the Friday 9AM session on Ontologies and Formal
Models at the meeting.  We will show how real SPARQL queries on
Darwin-SW-based data can address important competency questions
involving diverse linked resources.  Or see me any time during the
meeting earlier in the week and I'll be happy to give you a personal
demonstration not limited to 9 minutes.
Steve
[1]
http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html
see also open issue
https://code.google.com/p/darwincore/issues/detail?id=69
Robert Guralnick wrote:
...
Rod --- There are a couple different conceptions of
interrelationships between Darwin Core "classes", including the Darwin
Core Semantic Web effort led by Steve Baskauf and Cam Web, and the
BiSciCol project.  Darwin Core SW is
here: https://code.google.com/p/darwin-sw/ and the BiSciCol "take" is
here:  http://biscicol.blogspot.com/2013_03_01_archive.html.  The
Darwin Core SW version includes new classes not in Darwin Core, while
BiSciCol uses only existing class terms and a very simple set of
predicates.
I think in many people's view, including those of the authors of the
above (although I hate speaking for them), neither DW-SW or
DW-BiSciCol may be really able to handle the current needs for linking
resources together effectively.  There has been a major effort to
refocus away from jury-rigging Darwin Core to try to serve in a more
semantic framework and pushing towards other solutions that align
biodiversity standards more with the OBO Foundry
(http://www.obofoundry.org/).  The Biocollections Ontology
(BCO; https://code.google.com/p/bco/) represents (what I hope) is a
clear rethinking of the challenge that does connect back to the Darwin
Core.
Best, Rob
On Sun, Oct 13, 2013 at 1:52 PM, Roderic Page <r.page@bio.gla.ac.uk
mailto:r.page@bio.gla.ac.uk> wrote:
I've always been somewhat puzzled by the disconnect between the
TDWG LSID ontology
(e.g., http://rs.tdwg.org/ontology/voc/TaxonConcept ) which has a
rich set of classes and links between those classes, and Darwin
Core
(e.g., http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm )
which overlaps with this vocabulary and, in my opinion, does a
worse job in some areas, notably taxon names and concepts. Maybe
the LSID vocabulary suffered from the limited uptake of LSIDs
(apart from the nomenclators and Catalogue of Life) or from the
complexity of dealing with RDF, but it seems that much of the
essential work was done when Roger Hyam created that ontology.

What might help is a way to visualise the TDWG LSID ontology in
terms of the interconnections between the different classes. I'm
not aware of such a visualisation (nor of an equivalent one for
the Darwin Core classes).

In any event, it seems odd to have two distinct ontologies that
are both in use, and which overlap so significantly.

Regards

Rod
On 13 Oct 2013, at 16:12, Donald Hobern [GBIF] wrote:

...
It?s been a couple of weeks but I said I?d try to write something
about a more general concern I have around the way we use
basisOfRecord and dcterms:type to hold values like occurrence,
event and materialSample.  This is something that has concerned
me for years and that, I worry, is making everything we all do
much messier than it need be.

I believe that the way we have come to use Darwin Core
basisOfRecord is confused and unhelpful.  I really wish we used
Darwin Core like this:

1.       basisOfRecord should be used ONLY to indicate the type
of evidence that lies behind a record ? a key aspect of whether
the record is likely to be useful for different purposes
2.       basisOfRecord values should be taken from a hierarchical
vocabulary with three main branches:
a.       ?specimens? (i.e. biological material that can be
reviewed), with a hierarchy of subordinate values such as
?pinnedSpecimen?, ?herbariumSheet?, etc.
b.      derived, non-biological evidence (not sure what name),
with a hierarchy of subordinate values such as ?dnaSequence?,
?soundRecording?, ?stillImage?, etc.
c.       asserted observations with no revisitable evidence other
than the authority of the observer
3.       TDWG should deliver a basic ontology in the form of a
graph of key relationships between the most significant
conceptual entities in our world (TaxonName, TaxonConcept,
Identification, Collection, Specimen, Locality, Agent, ?)
4.       This ontology should not attempt to map all the
complexity of biodiversity-related data ? just provide the
high-level map and key relationships (TaxonConcept hasName
TaxonName, Specimen heldIn Collection, etc.) ? it should leave
definition of other properties as a separate, open-ended activity
for the community
5.       This ontology should be reviewed at regular intervals
and versioned as necessary to address critical gaps ? provided
that backwards compatibility is maintained (splitting a class
into multiple consitituent classes probably won?t break anything,
so start simple)
6.       The Darwin Core vocabulary should be published as a
flat, open-ended list of terms with clear definitions that can be
freely combined as columns in denormalised records
7.       Every Darwin Core term should be documented to be
tightly associated with a single, fixed class in the ontology
(e.g. scientificName and specificEpithet are ALWAYS considered to
be properties of a TaxonName whether or not that TaxonName object
is clearly referenced or separated out)
8.       Every data publisher should be encouraged to share all
relevant data elements in their source data in the most
convenient normalised or denormalised form, provided they use the
recognised Darwin Core properties for elements that match the
definition for those terms, and provided they give some metadata
for other elements.  Possible forms include:
a.       A completely hierarchical, ABCD-like, XML representation
b.      A completely flat denormalised, simple-DwC-like, CVS
representation, if the data includes no elements with higher
cardinality
c.       A set of flat, relational, CVS representations, as with
Darwin Core Archive star schemas, but with freedom to have more
complex graphed relationships as needed
9.       Each table of CVS data in 8b and 8c is a view that
corresponds to a linear subgraph of the TDWG ontology, identified
by the classes of the DwC properties used ? this allows us to
infer the ?shape? of the data in terms of the ontology
10.   If we do this, we do not need to worry about whether a
record is a checklist record, an event, an occurrence, a material
sample or whatever else, although we could use the dcterms: type
property, or some new property, to hold this detail as a further
clue to intent and possible use for the record

Here is an example.  In today?s terms, what sort of DwC record is
this?  Do I really have to replace ?recordId? with ?eventId?,
?occurrenceId? or similar? And which should I choose?

*recordId, decimalLatitude, decimalLongitude,
coordinatePrecision, eventDate, scientificName, individualCount*

I think it is clear that this record tells us that there was a
recording event at a particular time and place where someone or
some process recorded a given number of individual organisms
which were identified as representatives of a taxon concept with
a name corresponding to the supplied scientific name.  In other
words this gives us some properties from a subgraph that might
include, say, instances of TDWG Event, Locality, Date,
Occurrence, Identification, TaxonConcept and TaxonName classes.
None of these is specifically referenced but we can unambiguously
fold the flat record onto the ontology.  We can moreover then use
the combination of supplied elements to decide whether this
record would be of interest to GBIF, a national information
facility, a tool cataloguing uses of scientific names, etc.  The
same will also apply if multiple CVS tables are provided as in 8c.

I have thought about this for a long time and cannot yet think of
an area in which this would not work efficiently ? and
unambiguously ? for all concerned.  There are some cases where
multiple instances of the same ontology class would be referenced
within a single record, which may mean more care is needed by the
publisher (e.g. if an insect specimen record includes a reference
to a host plant). There may be cases where automated review of
the data indicates that there are impossible combinations or
ambiguities that the publisher must resolve.  However I believe
we could use this approach to generalise all mobilisation and
consumption of biodiversity data (including all the things we
have addressed under ABCD, SDD, TCS, Plinian Core, etc.) and to
make it genuinely possible for any data holder to share all the
data they have in a form that makes sense to them, while allowing
others to consume these data intelligently.

Right now, I think our confused use of basisOfRecord is almost
the only thing that stops us from exploring this.  We have
blurred the question of the evidence for a record, with the
question of the ?shape? of the record as a subgraph.  These are
different things.  Separating them will allow us to get away from
some of our unresolvable debates and open up the doors to much
simpler data sharing and reuse.

Thanks,

Donald

...
...
Donald Hobern - GBIF Director - dhobern@gbif.org
<mailto:dhobern@gbif.org>
Global Biodiversity Information Facility http://www.gbif.org/
GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?,
Denmark
Tel: +45 3532 1471 <tel:%2B45%203532%201471>  Mob: +45 2875 1471
<tel:%2B45%202875%201471>  Fax: +45 2875 1480
<tel:%2B45%202875%201480>

...
...
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---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email:  r.page@bio.gla.ac.uk <mailto:r.page@bio.gla.ac.uk>
Tel:  +44 141 330 4778 <tel:%2B44%20141%20330%204778>
Fax:  +44 141 330 2792 <tel:%2B44%20141%20330%202792>
Skype:  rdmpage
Facebook:  http://www.facebook.com/rdmpage
LinkedIn:  http://uk.linkedin.com/in/rdmpage
Twitter:  http://twitter.com/rdmpage
Blog:  http://iphylo.blogspot.com
Home page:  http://taxonomy.zoology.gla.ac.uk/rod/rod.html
Wikipedia:  http://en.wikipedia.org/wiki/Roderic_D._M._Page
Citations:
http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
<http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ>
ORCID:  http://orcid.org/0000-0002-7101-9767

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--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
PMB 351634
Nashville, TN  37235-1634,  U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582,  fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu

Re: [tdwg-content] A plea around basisOfRecord

Ramona Walls

Steve Baskauf

Ramona

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