Fundamental Niches, Distribution Areas and Presence-Only Data
Biodiversity Informatics, 7, 2010, pp. 17-44
ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY
RESOURCES BASED ON THE PROCESS OF THEIR CREATION AND THE
ROLE OF INDIVIDUAL ORGANISMS AS RESOURCE RELATIONSHIP
NODES
STEVEN J. BASKAUF
Department of Biological Sciences
Vanderbilt University, Nashville, TN, USA, steve.baskauf@vanderbilt.edu
Abstract. Kinds of occurrences (evidence of particular living organisms) can be grouped by common data
and metadata characteristics that are determined by the way that the occurrence represents the organism. The
creation of occurrence resources follows a pattern which can be used as the basis for organizing both the
metadata associated with those resources and the relationships among the resources. The central feature of
this organizational system is a resource representing the individual organism. This resource serves as a node
which connects the organism's occurrences and any determinations of the organism's taxonomic identity. I
specify a relatively small number of predicates which can define the important relationships among these
resources and suggest which metadata properties should logically be associated with each kind of resource.
Key words. GUID, individual, metadata, occurrence, RDF
Traditionally, biodiversity informatics has
involved the discovery and compilation of
specimen data, and the application of those data to
determine where organisms live. With the
development of computers and the Internet, the
capability now exists to aggregate and disseminate
biodiversity data globally as well as to broaden the
scope beyond that of establishing species ranges
(Kelling, 2008). Currently there is a coordinated
effort to create the data infrastructure, standardize
metadata terms (Darwin Core Task Group, 2009;
Jones et al. 2009), and develop persistent,
actionable identifiers (globally unique identifiers
or GUIDs; Cryer et al. 2009, Richards 2009) in
order to facilitate the aggregation of not only
specimen metadata, but metadata derived from
observations and digital representations of live
organisms such as images.
An important aspect of the development of
this global network is creating the capacity for
users (and the computer applications that assist
them) to find other resources that are related to a
resource which is at hand, i.e. "linked data"
1
.
Implicit in the concept of persistent identifiers is
the understanding such identifiers are also
resolvable, meaning that knowledge of the
identifier also provides a means to access the
information (data and metadata) for the resource to
1 http://www4.wiwiss.fu-berlin.de/bizer/pub/LinkedDataTutorial/
which the identifier refers. An important part of
this information is the relationship of the resource
to related resources, but using these links to
related resources is only possible if the
relationships are specified in a consistent way that
can be understood by all applications that wish to
use them.
In this paper, I suggest a system of organizing
biodiversity resources around individual organism
records. These records serve as nodes for
grouping related occurrence resources and their
taxonomic determinations. Because this system is
based on the way occurrence resources are created,
it connects the resources in a logically consistent
way and associates metadata properties with
resources in an efficient manner.
Definitions
In this paper, these terms are used according to
their standard meaning as a defined in the citations
or footnotes. The exceptions are abstract,
conceptual, and defined abstract resources which
for the purposes of this paper have been assigned
specific meanings as defined below.
resource - A physical, digital or conceptual
entity which can be identified by a Uniform
Resource Identifier (URI) (Berners-Lee et al.
2005).
information resource - A resource for which
all essential characteristics can be transmitted in a
mailto:steve.baskauf@vanderbilt.edu
http://www4.wiwiss.fu-berlin.de/bizer/pub/LinkedDataTutorial/
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
18
message (Jacobs and Walsh 2004), i.e. a digital
resource. Examples: text and digital images.
data - The content of the message that
provides the representation of the information
resource.
non-information resource - A resource that
cannot be transmitted electronically. Technically,
a resource is defined as a non-information
resource when an HTTP GET request for the
resource does not result in a 2xx "Success"
response, i.e. no data are returned (W3C Technical
Architecture Group 2005). Examples: persons,
specimens, observations, and taxonomic concepts.
metadata - Data about data
2
. All resources
can have metadata that describe their properties.
physical resource - A non-information
resource that is a material thing
3
. Examples: living
organisms, specimens, and 35mm slide images.
abstract resource - A non-information
resource that does not represent a particular
material thing. Examples: observations, protein
structures, state boundaries, and concepts.
conceptual resource - An abstract resource
that is subject to varying interpretation. Examples:
relationships, taxonomic concepts, and properties.
defined abstract resource - A resource which
represents a defined circumstance or abstract
object, and which therefore is not subject to
interpretation. Examples: observations,
determinations, and mathematical concepts.
HTTP URI - An identifier beginning with
"http://" used to name resources on the World
Wide Web ("the Web"). An HTTP URI may or
may not refer to a retrievable resource on the Web.
HTTP URIs uniquely identify a single resource.
node - A resource in a data structure which is
linked to other resources by references to them. In
diagrams in this paper, nodes are represented by
geometric shapes and the links between them are
represented by lines or arrows.
RESOURCES IN A BIODIVERSITY CONTEXT
Characteristics of occurrences resources
There are a number of categories of resources that
are of interest to the biodiversity community and
all of the types of resources defined above are
represented in these resource categories. The
primary focus of this paper is on resources that are
2 http://dublincore.org/metadata-basics/
3 http://purl.org/dc/terms/PhysicalResource
instances of the Darwin Core class Occurrence,
which is defined as "the category of information
pertaining to evidence of an occurrence in nature,
in a collection, or in a dataset (specimen,
observation, etc.)" (Darwin Core Task Group
2009). Although the name "Occurrence" suggests
that such resources serve the purpose of
documenting that an individual or population of
individuals occurred at a particular time and place,
categorizing a resource as an occurrence does not
imply fitness for that use or any other particular
use. An occurrence resource could also be used to
document character states, to serve as a type
specimen, to be used as a logo, or any combination
of these or other uses.
It should be clarified that the scope of this
paper is restricted to Occurrences as a subset of a
broader category of biodiversity resources defined
by Kelling (2008) as "observational data". The
scope of the paper includes observational data that
document the presence of a single individual at a
given point in time, but does not include
observational data that are place-based (e.g.
species checklists and measures of abundance;
Kelling 2008). For the purposes of this paper, an
occurrence is assumed to document a single
individual. However, most of what is discussed
here could also apply to small populations of
individuals that are of the same species.
Fig. 1. Components of a generic occurrence resource
What occurrence resources have in common is
that they assert that an organism occurred
somewhere at some time. In this paper, I will
describe the process by which occurrence
resources come into existence and how this
process can help us organize our thinking about
the relationship between resources and the
properties that should be associated with particular
types of resources. Determining the associations
and properties that are appropriate for particular
http://dublincore.org/metadata-basics/
http://purl.org/dc/terms/PhysicalResource
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
19
resource types is critical for the successful
implementation of an actionable GUID system.
In this paper I will distinguish between several
aspects of occurrence resources. Each occurrence
resource is the result of an event
4
which results in
the creation of the resource. During the event, a
representation of the organism may be created.
The resource and the possible representation with
which the resource may be associated have
properties that comprise the metadata for that
resource. Thus the occurrence resource may have
three aspects: a resource creation event, a
representation of the organism, and metadata (Fig.
1).
OCCURRENCE RESOURCE CREATION
EVENTS
In a resource creation event, the occurrence
resource must be created from another resource.
This follows from the fact that an occurrence
resource is evidence of the existence of an
organism. A resource such as a generic
illustration of a bird which is not created from
another particular resource is not an occurrence
because it does not represent a particular
organism. The resource creation event could itself
be considered a separate resource with its own
persistent identifier. However, because of the one-
to-one relationship between the creation event and
the created resource, it is more straightforward to
simply consider the metadata for the event (i.e.
time and location information) as a part of the
metadata for the occurrence resource itself.
When I say that a resource was "created" I
mean that the resource and any associated
representation was caused to become a separate
entity by whatever means is associated with that
particular type of resource. For example,
preserved specimens are collected, living
specimens are planted or moved from their natural
environment, digital images are photographed,
DNA sequences are sequenced, etc. This is not
saying that the creator necessarily caused the
representation itself to come into existence. For
example, a tree twig was actually "created" as a
physical object by the tree, not the person who
4 http://purl.org/dc/dcmitype/Event Note that the use of
"occurrence" in the definition of Event is in the sense of "something
happening" rather than the specific use of Occurrence sensu Darwin
Core.
collects it. However, the specimen that has the
twig as its representation of the tree was created
by the collector. Thus in this sense it is
appropriate for all occurrence resources to use the
Dublin Core (Dublin Core Metadata Initiative,
DCMI
5
) term dcterms:creator
6
("an entity
primarily responsible for making the resource")
7
to indicate the person (or institution) who caused
the resource to come into existence.
It is also important here to make the
distinction between the event that results in the
creation of the occurrence resource and the
occurrence resource itself. For some resources,
this distinction is obvious. For example, when a
specimen is collected, there is an event (a segment
of a collecting trip) that takes place at a particular
time and place and the result of this event is a
resource that we call a specimen. When an image
of an organism is recorded, an event (a "photo
shoot") that takes place at a particular time and
place results in a resource we call a StillImage.
Unfortunately this distinction is blurred in the case
of an observation because we use the word
"observation" to mean at least two different kinds
of things. Webster's New World Dictionary
provides two definitions of "observation" as "4 a)
the act or practice of noting and recording facts
and events, as for some scientific study b) the data
so noted and recorded" (Neufeldt and Guralnik
1994). The first definition (a) represents an
observation as an event (as in "we conducted an
observation") and the second (b) represents an
observation as the created resource (as in "our
observations were written in a notebook").
Observation occurrences are resources of the
second type. They have resource creation events,
but they are not themselves events. (It is
sometimes suggested that observation occurrences
should be classed in the Dublin Core class Event,
but they are no more events than are specimens or
images). In the remainder of this paper, unless
otherwise noted use of the term "observation" is
intended to represent sense (b).
5 http://dublincore.org/
6 Namespace http://purl.org/dc/terms/
7 http://purl.org/dc/terms/creator
http://purl.org/dc/dcmitype/Event
http://dublincore.org/
http://purl.org/dc/terms/creator
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
20
Fig. 2. Comparison of the components of the three
general categories of occurrence resources.
ORGANISM REPRESENTATIONS
ASSOCIATED WITH OCCURRENCE
RESOURCES
Occurrence resources fall into three of the general
categories listed in the definitions section based on
the nature of the way in which they represent the
organism (Fig. 2, Table 1). These categories are
natural divisions that are based on whether and
how a consumer can retrieve a digital
representation of the organism from which the
resource is derived.
There are several general points regarding
these categories of occurrence resources.
Regardless of whether a digital representation is
ultimately available, all three of these types of
resources have associated metadata and they have
many metadata terms in common. Thus despite
their differences in representation, metadata from
these three types of resources can be combined in
the same database.
It should also be stated explicitly that in the
case of physical resources, it is desirable to create
information resources that provide Internet-
deliverable representations of the material
artifacts. This is generally recognized and much
effort has been expended toward digitization of
physical resources. Thus it follows that a
conceptual system describing occurrence resources
must be able to relate physical resources to
information resources that are derived from them.
The definition of an observation resource
given here is a functional one, i.e. if an occurrence
resource can never ultimately provide a digital
representation of the organism, then it is an
observation resource. This definition is consistent
with other definitions of observations that are not
explicitly based on the ultimate result of an HTTP
GET request. The Biodiversity Information
Standards (TDWG) Observations Task Group
provides a working definition of observational
data:
"… the outcomes of acts of measurement using
particular protocols within the context of any
objective scientific measurement activity.
Examples include data from survey or monitoring
efforts, controlled experiments, and sensor-derived
measurements. In each case, the basic or atomic
notion of an observation represents the outcome of
some measurement taken of a defined attribute or
characteristic of some 'entity' (e.g., an organism 'in
the field', a specimen, a sample, an experimental
treatment, etc.), within some context (possibly
given by other observations). Every observation
entails the measurement of one or more properties
of some real-world entity or phenomenon."
8
This definition makes two major points. One
is that object of observations includes real world
entities, including organisms in the field,
specimens, and samples. The other is that
observations measure defined attributes or
characteristics. To place these statements in the
formal language of URI-identified resources,
observations establish values of properties that
describe resources which can include occurrences
(sensu Darwin Core). An important implication of
this is that as defined here, observation resources
record metadata (i.e. data about resources that can
be described using language such as Resource
Description Framework, RDF) and not data in the
sense of what is returned in the resolution of a
8 http://wiki.tdwg.org/Observational/
http://wiki.tdwg.org/Observational/
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
21
Table 1. Categories of occurrence resource and their associated representations
resource category how an organism
is represented by
that category
specific representations how a consumer can
acquire a representation of
the organism
information
resource
by a digital file digital image
digital audio
digital video
DNA sequence
HTTP GET returns data
which is the representation
in digital form
physical resource by a material
artifact
film photograph
film movie
audiotape sound recording
preserved specimen
living specimen
seed
tissue sample
HTTP GET does not return
data, but a redirect may
ultimately result in access to
an information resource that
is a representation derived
from the artifact
observation
resource (kind of
defined abstract
resource)
no representation none HTTP GET returns nothing.
No redirect can result in
return of a representation.
GUID. This concept is explicitly stated in Pereira
(2009) which states that "core objects in
biodiversity information systems such as …
observations are not associated with immutable
sequence of bytes that could be returned in the
LSID getData() call. It is reasonable not to return
anything in the getData() call." This concept of
observation resources places them in the category
of abstract resources (because they are not
associated with a corresponding material object),
although not in the category of conceptual
resources (because the observation is a defined
entity that is not subject to interpretation). This
concept of an observation is also narrower than the
general category of "observational data" as defined
by Kelling (2008).
The TDWG Observation Task Group
definition of "observation" also includes metadata
resulting from measurements of specimens and
samples. However, in the system for categorizing
resources presented here, such observations would
not themselves be considered to be metadata for
separate observation resources, but rather metadata
associated with other resources that are physical.
By the functional definitions in Table 1, a numeric
measurement of an organism in the field (e.g. a
measured bill length of a bird) could be considered
an information resource if the measurement is
considered a very simplified representation of the
organism and is an immutable series of bytes (i.e.
data as opposed to metadata which are subject to
change). The important point is that the functional
categorization of the three general types of
Occurrence resources determines the kinds of
metadata that one should expect for them and the
way that those metadata should be organized.
METADATA ASSOCIATED WITH ALL
OCCURRENCE RESOURCES
Despite the differences among the three general
categories of occurrence resources, they all have
several properties in common. The metadata
records for all occurrence resources should include
a globally unique identifier (dwc:occurrenceID),
information about who created the resource
(dcterms:creator), information about when the
resource creation event occurred
(dcterms:created), information about where the
resource creation event occurred (location
information), and information about the particular
nature of the resource. This summarizes in the
most basic way the "who, what, where and when"
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
22
desired by the Global Biodiversity Information
Facility (GBIF)
9
.
Recently, much effort has been exerted to
establish precise location information for
occurrence records, i.e. to geolocate them
(Chapman and Wieczorek 2006). The ultimate
goal of this effort is to create descriptors of
location that are unambiguous and mappable by
software. For newly created occurrence resources
or those which have been precisely geolocated, the
following set of four Darwin Core terms (dwc:
10
)
unambiguously define the location where the
occurrence occurred: dwc:decimalLatitude,
dwc:decimalLongitude, dwc:geodeticDatum, and
dwc:coordinateUncertaintyInMeters
11
. The first
two terms define the numeric coordinates of the
location, the third term describes the reference
system used (for GPS measurements the default
reference system is WGS84 which has the EPSG
code of EPSG:4326
12
; "unknown" is also a valid
value), and the fourth term provides an estimate of
the uncertainty of the measurement. A fifth term,
dwc:locality, provides a verbal description of the
location at the lowest geographic level. A locality
description is important because it can make it
easier for an observer on the ground to return to
the location and because it can be used to validate
the coordinates (Chapman and Wieczorek 2006).
Darwin Core also provides many other terms to
describe location using large-scale geographic and
political subdivisions and these descriptors may be
included in an occurrence record along with the
five terms listed above. Since the values of those
additional terms may be subject to change over
time as political boundaries and names change,
and because they can theoretically be generated by
software from the four basic mathematical terms,
they should be considered of secondary
importance. However, for older pre-existing
records it may be difficult or impossible to
establish a precise location for the occurrence. In
such cases, the additional terms may be the only
means available for specifying location.
A description of the nature of the resource is
important in order to help potential users of the
metadata to assess the fitness of the resource for
9 http://www.gbif.org/
10 Namespace http://rs.tdwg.org/dwc/terms/
11http://code.google.com/p/darwincore/wiki/Location#verbatimLati
tude,_verbatimLongitude
12 http://spatialreference.org/
their intended use. There are three terms that can
be used to specify the nature of a particular
resource. The property rdfs:type
13
has been
designated as the means by which the nature of the
biodiversity resource should be specified to
consuming applications (example given in Pereira
et al. 2009). Since resources should be typed
according to the TDWG ontology "or other
accepted vocabularies" (Richards 2009), the
TDWG ontology class TaxonOccurrence
14
is the
appropriate value of rdfs:type for occurrence
resources. The term dcterms:type
15
is well
known beyond the biodiversity community and
has a defined type vocabulary
16
. The values
PhysicalObject, StillImage, MovingImage, and
Sound are appropriate for occurrence resources.
However, there is no dcterms:type vocabulary
term that adequately describes observation
resources. The property dwc:basisOfRecord
17
provides a more specific description of the
resource than dcterms:type and uses a defined type
vocabulary
18
that is designed particularly for the
biodiversity community. Those terms describe
many of the kinds of resources that are
occurrences and include PreservedSpecimen,
FossilSpecimen, LivingSpecimen,
HumanObservation, and MachineObservation.
METADATA ASSOCIATED WITH
SPECIFIC CATEGORIES OF
OCCURRENCE RESOURCES
Physical resources are distinguished from other
occurrence resources by the physical artifact that
represents the organism. Therefore, the metadata
that are most relevant to a physical artifact answer
the question "How can I find/look at/get the
artifact?" In a biodiversity context, physical
artifacts are generally a part of
museum/herbarium/botanical garden/zoo
collections, so all of the terms related to where and
how these artifacts are stored in a collection are
relevant exclusively to physical resources.
Information resources are the only category of
occurrence resources where the representation
13 http://www.w3.org/2000/01/rdf-schema#type
14http://rs.tdwg.org/ontology/voc/TaxonOccurrence#TaxonOccurre
nce
15 http://dublincore.org/documents/dcmi-terms/#terms-type
16 DCMI Type Vocabulary section of
http://dublincore.org/documents/dcmi-terms/
17 http://rs.tdwg.org/dwc/terms/index.htm#basisOfRecord
18 http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm
http://www.gbif.org/
http://code.google.com/p/darwincore/wiki/Location%23verbatimLatitude,_verbatimLongitude
http://code.google.com/p/darwincore/wiki/Location%23verbatimLatitude,_verbatimLongitude
http://spatialreference.org/
http://www.w3.org/2000/01/rdf-schema#type
http://rs.tdwg.org/ontology/voc/TaxonOccurrence#TaxonOccurrence
http://rs.tdwg.org/ontology/voc/TaxonOccurrence#TaxonOccurrence
http://dublincore.org/documents/dcmi-terms/%23terms-type
http://dublincore.org/documents/dcmi-terms/
http://rs.tdwg.org/dwc/terms/index.htm%23basisOfRecord
http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
23
itself can be stored and distributed electronically.
Thus, the foremost requirement for a digital
resource is that the digital representation exists as
data (i.e. a retrievable file of immutable bytes)
from at least at one location in the Internet. In
addition to the URL from which the data can be
retrieved, metadata terms that specify the format
of the data and the circumstances under which the
information resource can be used (i.e. copyright,
licensing, and attribution information) are
important. The TDWG/GBIF Multimedia
Resources Task Group (MRTG)
19
draft standard
metadata schema
20
is appropriate for occurrence
information resources and its recommendations
should be followed.
Since observation resources have no
representation associated with them, there are no
specific metadata terms required to describe the
representation as is the case for physical and
information resources. Since the focus of most
observations is measurement data, specifying the
properties, format, and units of the measurements
will be important aspects of observation resources
metadata.
OCCURRENCE RESOURCE
CREATION NETWORKS
General patterns in occurrence resource creation
In the previous section it was established that
various categories of occurrence resources are
created from other resources during resource
creation events and that it is sometimes desirable
to create other occurrence resources from those
occurrence resources. These relationships can be
diagrammed generally by Fig. 3.
The following points can be made about the
relationships among occurrence resources:
1. Every occurrence resource must have a resource
from which it is derived during a resource
creation event.
2. Every occurrence resource is the result of a
single resource creation event.
3. An occurrence resource may serve as the source
of one or more derivative occurrence resources,
or it may have none.
4. An occurrence resource may be associated with
a physical/digital representation of an organism.
If it has no representation, it is considered in this
context to be an observation resource.
19 http://www.keytonature.eu/wiki/MRTG
20 http://www.keytonature.eu/wiki/Submission_v0.9
5. An occurrence resource which is an information
resource may be derived from either a physical
resource or another information resource.
6. An occurrence resource which is a physical
resource will only be derived from another
physical resource. (There may be trivial
examples where a physical resource could be
derived from an information resource, such as a
paper print of a digital image. But since a
general goal is to create distributable electronic
representations of physical representations,
information resources generally reside at the end
of a chain of resource creation.)
7. An occurrence resource which is an observation
resource cannot be derived from a representation
associated with an information or physical
occurrence resource. If one were to make
"observations" of a physical or information
occurrence resource (e.g. to take measurements
from a specimen or image) those "observations"
would be metadata that should be associated
with the representation, and should not be
considered a separate observation occurrence
resource. Thus observation resources can only
be derived directly from an organism.
8. Information or physical occurrence resources
cannot be derived from observation resources
because a digital or physical representation
cannot be created from something that has no
representation.
INDIVIDUALS AS THE ULTIMATE
SOURCE OF OCCURRENCE RESOURCES
Although an occurrence resource can be derived
from another occurrence resource, ultimately all
occurrence resources must originate through their
chain of derivation back to an organism in its
environment. I call this original organism an
"individual" because it plays the role described in
the definition of the Darwin Core term
dwc:individualID
21
, "an identifier for an individual
or named group of individual organisms
represented in the occurrence. Meant to
accommodate resampling of the same individual
or group for monitoring purposes. May be a
global unique identifier… ". In clonal species or
small species such as mosses, it may be difficult to
determine whether samples collected at a
21 http://rs.tdwg.org/dwc/terms/individualID
http://www.keytonature.eu/wiki/MRTG
http://www.keytonature.eu/wiki/Submission_v0.9
http://rs.tdwg.org/dwc/terms/individualID
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
24
Fig. 3 Generic relationships among a focal occurrence resource and other resources related to it
particular location were collected from a single
organism or a small population of organisms of the
same species. Thus a group of organisms of the
same species in the same location may be
considered an "individual" even if technically they
are several individual organisms.
If an individual were always represented by a
single occurrence resource, then considering the
individual to be a separate resource would be
superfluous. Properties related to taxonomic
identity could as easily be associated with the
occurrence resource as they could be associated
with the individual. However, it is possible for a
single individual to be observed, sampled, or
imaged multiple times or to be represented by
several different types of occurrence resources. It
would be redundant to assign the same taxonomic
identity metadata to multiple occurrence resources
derived from the same individual rather than to
assign those metadata to the individual and then
link the occurrence resources to the individual. In
addition, it would be inconsistent to make a
determination of one taxonomic identity for one
occurrence resource and make a different
determination of identity based on and assigned to
another occurrence resource derived from the
same individual. That individual can only have a
single identity, so any determinations assigned
based on one resource should apply to all other
resources derived from the same individual. The
most straightforward way to ensure this is to
assign the determinations to the individual rather
than to the separate occurrence resources.
The resource representing a wild individual
can also connect determinations to resources
derived from organisms other than that individual
if those organisms arise from the individual
through cloning (e.g. vegetative propagation) or
even sexual reproduction. Those additional
derivative organisms (which generally would
generally not be in their natural environment and
would therefore be classified as living specimens)
must have the same taxonomic identity as the wild
individual from which they originate, so any
determination based on a derivative organism must
apply to the individual itself and all other
organisms derived from it.
SOME EXAMPLES OF RESOURCE
CREATION NETWORKS
The following four figures illustrate some
examples of increasingly complex networks of
resource creation.
Fig. 4 illustrates the types of resources
involved in a classical museum collection. In this
situation an herbaceous plant is collected in its
entirety, so when the preserved specimen is
created, the individual ceases to exist in the
environment. It is easy to consider the plant and
the specimen to be one and the same thing.
Because of the simplicity of this network, a simple
and flat table in a database can be used to compile
the data/metadata associated with specimens of
this type. In a typical herbarium, the specimen is
assigned a taxonomic identity (name) and the
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
25
Fig. 4. Diagram showing the relationships among an individual, resources derived from it (a specimen and a
specimen image), and the resources' associated creation events in a classic museum collection scenario.
plant's location is noted in the database for the
specimen. Later, the specimen is imaged and a
single reference to the image is made in the
database record for the specimen. In such a
scenario, there is little benefit to considering the
individual to be a separate resource because nearly
all relevant metadata can be associated with the
specimen.
In Fig. 5, an insect is located in a field survey.
Before the insect is collected and killed, it is
photographed live in its environment with a digital
camera. After the survey trip, the insect is pinned
and added to the museum's collection. As a part of
the museum's efforts to document its collection,
the pinned specimen is imaged digitally. The
museum is also supporting a molecular
systematics effort and donates a small sample
from the insect from which DNA is extracted,
sequenced, and submitted to GenBank. Later, as a
part of an effort to develop a database of
characters, the pinned specimen is dissected
andseparate specimens are created of various body
parts, which are then digitally photographed under
a microscope. The original pinned specimen
ceases to exist as an entity upon the creation of the
separate part specimens. As they have now
become a permanent part of the collection, the
separate part specimens are assigned their own
catalog numbers.
Fig. 6 represents a hypothetical collection
scenario for a botanical garden. During a field
expedition, a survey crew locates an unusual tree
and takes a number of digital images of the tree.
A botanist on the team reviews the images and
tentatively identifies the tree as a rare species. The
survey crew returns to collect cuttings for
propagation and branch/leaf specimens from the
tree for the botanical garden's herbarium. Another
team returns later in the season after fruit has set
and collects seeds. Part of the seeds are imaged
and stored as a part of an effort to preserve
germplasm of rare species. Other seeds are
germinated and the resulting plants are added to
the garden's permanent collection. DNA is
collected from one of the living specimens in the
garden and the DNA sequence is submitted to
GenBank. Additional herbarium specimens may
be collected from the living specimens in addition
to those collected from the original tree and other
individuals may be vegetatively propagated and
sent to other botanical gardens. Although the
various botanical garden specimens are separate
organisms from individual in the wild, those living
specimens are derived clonally or genetically from
the individual in the environment and thus can
provide information regarding the wild
individual's taxonomic identity.
Fig.7 involves an effort to track an individual
of a large, rare species of bird (e.g. whooping
crane). The young bird is initially observed
visually in the nesting ground and recorded in an
ornithologist's field records. Several days later the
decision is made to capture and band it. The
following year, the information from the band is
recorded by a different ornithologist in the
overwintering grounds. At a later time the bird is
recaptured. A tissue sample is collected for DNA
extraction and analysis and the bird is fitted with a
radio tracking device. Data/metadata are collected
throughout migration using telemetry from the
tracking device.
Historically, biodiversity records have been
organized around specimens. In a simple scenario
such as Fig. 4, this is practical. However, in Figs.
5-7, occurrence information resources (i.e. images)
are collected directly from the individual and are
not derived from any specimen. In Fig. 7, no
specimen is collected at all. Thus in any collection
scenario more complicated than Fig 5 it makes
sense to consider the individual as an identified
resource (i.e. having an assigned GUID).
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
26
Fig. 5. A more thorough museum collection scenario involving an insect specimen.
METADATA ASSOCIATED WITH
INDIVIDUALS
In previous sections it was noted that metadata
associated with occurrence resources describes
where, when, and by whom the resource was
created as well as the nature of the resource itself
and how any representations associated with the
resource can be accessed. Since an individual is
by definition in its natural state (any individual
taken out of its natural state would become a
living specimen), no human entity can be assigned
as its creator.
Although an individual could be considered to
have had a time of creation (i.e. when it was born,
hatched, or germinated), it is not possible to know
when nor where this occurred without creating an
occurrence resource. If the time of the organism's
birth were noted by a human observer, then an
observation resource would be created with the
time of birth represented by the resource creation
event metadata for the observation resource. If the
birth were digitally imaged, then an information
resource (StillImage) would be created. It is, in
fact, not possible to know anything about any time
of existence or location of an individual without an
occurrence resource creation event occurring. For
this reason, particular dates and locations of events
should not be assigned to an individual. However,
it would be possible, if desired, to assign to the
individual the set of dates and locations for all
resource creation events resulting in resources
derived directly from the individual. Such a set
can be considered to define the spatial and
temporal range of that individual. In Figs. 4-7,
such resource creation events originating directly
from individuals are highlighted in gray.
In addition to the conceptual reason why
location should be associated with derived
occurrence resources rather than the individual
organism, there are also several practical reasons.
Foremost among these is that some organisms
move, and since some resource creation events
(those creating observations and images) do not
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
27
Fig. 6. Collection scheme for a botanical garden.
necessarily result in the destruction of the
organism and the fixing of its location at the point
of death, it may not be possible to assign a single
location to a mobile organism. Therefore, the set
containing all locations where occurrence
resources were created directly from an individual
represents the geographic range of that moving
individual.
It also makes sense to record multiple resource
creation locations even for sessile organisms. For
example, an individual plant may be imaged
several times by a GPS-enabled digital camera.
Because of inaccuracies in the determination of
latitude and longitude recorded with the images,
each location recorded by the camera represents an
estimate of the actual location of the individual. In
that situation, the set containing all locations
where resource creation events occurred allows
determination of a sort of "standard error" of
location. It is also possible that locations
associated with the creation of different resources
from the same individual may have different
precisions. For example, a specimen may first be
collected from a tree and the tree's location
determined by reference to a topographic map. At
a later time, a digital image may be taken of the
same tree with the tree's location determined by
GPS. The precision of the GPS determination is
likely to be greater than the determination from the
map, so it would be important to maintain both
sets of geographic coordinates along with their
precisions so that a user could assess the relative
utility of each for re-locating the tree.
For the reasons given above, it is clear that
location is logically an aspect of the creation event
of each particular occurrence resource. However,
it should be noted that since some occurrence
resources may not be directly derived from an
individual organism in its natural state, it cannot
necessarily be inferred that an occurrence resource
creation event contributes to documenting the
distribution of a taxon. For example, a preserved
specimen may not indicate the presence of a taxon
representative at the place of its creation if it was
collected from a living specimen in a botanical
garden. A digital still image may not indicate the
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
28
Fig. 7. Bird survey based primarily on observations.
presence of a taxon representative if it is an image
of a specimen, while it may if it is a picture of a
living individual in the wild. There is currently no
term in the Darwin Core standard that is suitable
for indicating unambiguously that the date and
location of an event serves to document a taxon
distribution. It can be established from the
metadata that an event asserts that a representative
of a taxon was present at the location of an
occurrence resource creation event if the identifier
for resource from which occurrence is derived is
the same as the identifier of the individual that the
occurrence represents. However, to serve the
purpose of clarifying whether the resource creation
event of an occurrence documents the distribution,
the term sernec:documentsDistribution
22
has been
defined.
It should also be made clear that the typing of
an occurrence resource using dcterms:type,
rdfs:type, or dwc:basisOfRecord does nothing to
restrict fitness of use of that resource to any
particular purpose. Regardless of whether or not
an occurrence resource is used to establish that a
22http://bioimages.vanderbilt.edu/rdf/terms#documentsDistribution
; appropriate text values are "true" or "false"
taxon representative is present at a location, there
is no restriction prohibiting that occurrence
resource from simultaneously being used for any
of a number of purposes, e.g. to define a character,
as a learning tool, to illustrate a habitat, to serve as
a type specimen, etc. Fitness of use for such
purposes may be noted through the inclusion of
appropriate properties in the metadata for the
occurrence resource - there is no limit to the
number of such properties that may be included.
It is useful at this point to differentiate
dcterms:creator from the Darwin Core term
dwc:recordedBy. As discussed in the section on
resource creation events, in the context of
occurrences, dcterms:creator represents the entity
that caused any occurrence resource to come into
existence. dwc:recordedBy is a "list … of names
of people, groups, or organizations responsible for
recording the original occurrence". Thus
dwc:recordedBy carries the additional connotation
that the resource created by creator of an "original
occurrence" (i.e. a resource created directly from
an individual -- a resource creation event
represented by a gray arrow in Figs. 4-7) can be
used to establish the presence of a taxon at a
http://bioimages.vanderbilt.edu/rdf/terms%23documentsDistribution
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
29
location. Thus occurrence resources derived
directly from individuals
(sernec:documentsDistribution value="true") will
usually have values for both dcterms:creator and
dwc:recordedBy, while resources not derived
directly from individuals
(sernec:documentsDistribution value="false") will
have no value for dwc:recordedBy. The same
criteria hold for dcterms:created and
dwc:eventDate. If a resource is derived directly
from an individual, it should be given identical
values for dcterms:created and dwc:eventDate,
while a resource not derived directly from an
individual should only be assigned a value for
dcterms:created.
The only general category of metadata that
should logically be associated with individuals is
information related to taxonomic determinations.
As we shall see later, there is benefit to
considering these determinations as separate
resources rather than as metadata of the resource
representing the individual. Thus individuals as
resources serve primarily as nodes that connect
their derivative occurrence resources to taxonomic
determinations. With few exceptions, the
metadata for resources representing individuals
will consist primarily of statements indicating the
relationship of that individual to other resources.
One such exception would be assignment of a
value for dwc:establishmentMeans to indicate
whether the individual was native, naturalized,
adventive, or cultivated.
RELATIONSHIPS AMONG
DATA/METADATA RESOURCES
Relationships Networks
The conceptual scheme of resource creation was
focused on networks which traced the series of
events by which occurrence resources of various
types were created from individual organisms. In
this section, I will focus on the relationships
among resources of various kinds and the ways
those relationships can be specified.
In Fig. 8, each shape represents a resource as
defined in the definition section. Each line
represents an important relationship between two
resources in the network. The heavy lines below
the individual represent the connections
established between pairs of resources by the
occurrence resource creation events discussed
previously. A given focal occurrence resource is
connected by the line above to the resource from
which it was derived. Lines below the resource
connect it to occurrence resources that were
derived from it.
Since taxonomic identity is a property of the
individual organism, the individual should have
one or more determinations which link that
individual with a general taxonomic concept
(Franz 2008), identified as "taxon" in Fig. 8. Each
determination may be considered a unique,
defined abstract resource linked to that individual
and having its own assigned GUID
(dwc:identificationID). The taxonomic concept
(dwc: taxonConceptID) to which the
determination is linked is a conceptual resource
that may be applied to many determinations and
which has its own HTTP URI (e.g. DeVries,
2009). The taxonomic concept itself may be
linked to one or more scientific and vernacular
names (not represented in Fig. 8) which may be
considered separate abstract resources having
complex relationships among themselves (Page
2006).
In common usage, an initial determination
may be called the "identification" and subsequent
determinations may be called "annotations".
However, regardless of order, each determination
represents a functionally equivalent assessment of
the individual's identity, having properties of
dcterms:created, dwc:identifiedBy,
dwc:identificationRemarks, etc. Each
determination has a relationship with one or more
resources that served as the evidence by which the
determination was made. This "determination
based on" relationship is represented by the small-
dashed lines. It should be noted that a
determination has a particular resource (or
resources) on which it is based, but particular
resources do not have a particular determination
that represents the identity of their source
individual. The resource is a representation of the
individual and the individual will have all of the
determinations as possible assessments of its
identity.
Since taxonomic identity is assigned to a
resource through its relationship with the
individual, this identity must be accessed via the
individual at the root of the resource creation
chain. The individual can be located by following
the lines through resources up the derivation chain.
However, it may be convenient to specify directly
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
30
Fig. 8. Network of important relationships among resources in a complex resource creation scheme. Occurrence
resources could represent some of those in Fig. 6 (I=tree in environment, O1=seed, O2=botanical garden
specimen, O3=GenBank accession, O4=live plant image, O5=herbarium specimen, O6=herbarium specimen
image).
the source individual from which the resource was
ultimately derived. The "source individual"
relationship for each derived resource is indicated
by the long-dash lines.
SPECIFYING RELATIONSHIPS
BETWEEN RESOURCES - RESOURCE
DESCRIPTION FRAMEWORK (RDF)
The links among resources discussed in the
previous section can be defined formally using
Resource Description Framework (RDF)
23
, which
has a well-defined syntax for representing
resources and relationships. RDF can be
represented several ways
24
. Relationships can be
shown as graphs, while RDF serialized as XML
25
is also the default means for describing metadata
when a GUID is resolved (Richards 2009).
Figs. 9-11 show RDF graphs for examples of
three of the major types of resources diagrammed
in Fig. 8 (the fourth, taxonomic concept, is beyond
the scope of this paper). In these graphs, ovals
represent resources named by HTTP URIs.
23 http://www.w3.org/RDF/
24 http://www.w3.org/TR/rdf-primer/
25 http://www.w3.org/XML/
Rectangles represent literals (composed of
Unicode characters). The resource in the center of
the graph is the subject of the relationships. Each
arrow in the graphs represents the nature of the
relationship (referred to as a "predicate" in RDF)
with a description of that relationship next to the
arrow. The objects of the relationships (shapes
pointed to by the arrows) are the metadata
associated with the subject (the object of the
relationship).
In many cases, the predicate describing the
relationship is a property that is a term from a
well-known vocabulary. In particular, the
following prefixes are used for qualified
namespaces representing these vocabularies.
dcterms="http://purl.org/dc/terms/"
dwc="http://rs.tdwg.org/dwc/terms/"
In addition, there are several terms for
relationships described in this paper but which
have not previously been defined. These terms
have been formally defined in RDFS
26
and they
have been assigned to the qualified namespace:
26 http://bioimages.vanderbilt.edu/rdf/terms
http://www.w3.org/RDF/
http://www.w3.org/TR/rdf-primer/
http://www.w3.org/XML/
http://bioimages.vanderbilt.edu/rdf/terms
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
31
Fig. 9. RDF graph for an occurrence resource (based on relationships outlined in Fig. 8)
Fig. 10. RDF graph for an individual (based on relationships outlined in Fig. 8)
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
32
Fig. 11. RDF graph for a determination (based on relationships outlined in Fig. 8)
sernec="http://bioimages.vanderbilt.edu/rdf/ter
ms#"
These terms are:
derivedFrom Indicates the resource
from which the subject (an occurrence resource)
was derived. May be an individual or another
occurrence resource
derivativeOccurrence Indicates an
occurrence resource that was derived from the
subject (the subject may be an individual or an
occurrence resource)
identifiesIndividual Indicates an
individual that is identified by a determination
basedOnOccurrence Indicates an
occurrence resource used as the basis for a
determination.
usedInDetermination Indicates a
determination for which the subject (an occurrence
resource) was used as a basis for identification
The properties of an occurrence (Fig. 9;
Appendix A) fall into four general categories. The
first includes general descriptive metadata that
applies to all resources, such as the GUID of the
resource, and a dcterms:description of what it is.
The second is general metadata that applies to all
occurrence resources, as described in the section
"Metadata associated with all occurrence
resources". Other metadata terms related to
occurrences may be included if necessary or
desired. The third category of metadata is that
which applies to the specific kind of occurrence
(Table 1). In general, information resources
require metadata describing intellectual property
rights, and use and attribution guidelines described
in the MRTG schema. Physical resources may be
described using specific Darwin Core terms which
apply to that type of occurrence. The fourth
general category is properties that describe how
the occurrence resource is related to other
resources. These properties relate the resource to
other resources from which it is derived or which
are derived from it, determinations that are based
on that occurrence, and the individual from which
the resource is ultimately derived.
In the example of Fig. 9 (and its corresponding
Appendix A), literals were used for the values of
properties referring to entities (persons and
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
33
institutions). However, HTTP URI references
could also be used and would be preferable if they
represented a "semantic web-aware" resource
(such as a FOAF
27
file) that can be de-referenced.
The metadata of an individual (Fig. 10;
Appendix B) consists almost entirely of properties
that define the relationships between the individual
and resources derived from it, and the individual
and determinations that assign the individual to a
taxon concept. This highlights the role of an
individual as a node that connects other resources.
One property of the individual that is assigned a
literal value is dwc:establishmentMeans, which
can be used to indicate whether the individual is
wild or cultivated.
The metadata of a determination includes a
description of who made the identification and
when. But the most important aspect of the
determination metadata is a description of the
connections formed by the determination between
an individual and a taxon concept that is consistent
with the facts of the individual as illustrated by its
occurrences. This connection is supported by
including links to the occurrence resources on
which the determination was based. If those
occurrences are information resources, a user
could examine them to verify the determination.
One advantage of this system of organization
is that it requires very few predicates to define the
relationships among occurrence resources,
individuals, and their determinations. By using
generic descriptions of relationships followed by
tagging
28
, the overall system is simpler than the
alternative of creating different relationship types
for different kinds of object resources. For
example, sernec:derivativeOccurrence is used
rather than creating separate predicates for each
type of derivative occurrence object (e.g. rather
than using dwc:associatedMedia and
dwc:associatedSequences specifically to indicate
images and sequences derived from specimens and
tissue samples). Similarly, by considering both
identifications and annotations as one type of
resource (determination), a single predicate can be
used to indicate the relationship of another
resource with the determination. If desired, an
application can infer which determination is the
27 http://www.foaf-project.org/
28 http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot
initial identification by finding the determination
with the earliest dwc:dateIdentified value.
It should also be noted that relationships
involving an occurrence resource do not have to be
limited to those illustrated here. For example,
nodes representing habitat sites or character
definitions could group occurrence resources
derived from different individuals. Appropriately
defined predicates could link the occurrence
resources to those nodes through entries in the
RDF XML file for the occurrence. The
relationships outlined here represent the minimum
set of relationships that are needed to establish the
taxonomic identity that should be associated with
the occurrence and to link the occurrence to others
that are closely related to it.
CONCLUSIONS
The role of individuals.
Resources representing individuals serve as
nodes which connect multiple occurrence
resources that are derived from that same
individual, such as duplicate specimens, direct
images of the live organism, and multiple
observations. They also provide a single resource
to which determinations can be assigned, avoiding
the necessity of repeating identification metadata
in all of the occurrence records for the same
organism and insuring that annotations are applied
to all of those occurrences. One deficiency of the
conceptual scheme described in this paper is that it
does not adequately handle circumstances where a
single occurrence resource contains evidence of
multiple individuals. Examples would include the
contents of a pitfall trap which included several
insects, an image of a habitat showing several
individuals of different species, and a specimen of
an organism that showed evidence of parasitism
by an individual of a different species.
Clarification of artifact types and their
relationships to resource classes.
By explicitly categorizing occurrence
resources according to the nature of their
representation of an organism (physical, digital, or
none), it becomes clearer which metadata elements
are most appropriately assigned to various
particular kinds of occurrence resources. This
categorization also makes it clear in the process of
GUID resolution what metadata should be
http://www.foaf-project.org/
http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
34
expected by a consuming application for those
kinds of resources.
Clarification of what determines that an
occurrence provides information about the
presence of a representative of a taxon at a
location.
It is clear from Figs. 4-7 that occurrence
resources assert that a taxon representative is
present at a location if the occurrence resources
were derived directly from the individual (i.e. gray
arrows) and not because those resources are of any
particular kind. This clarification can be made
explicit through use of the term
sernec:documentsDistribution.
Role of resource creation networks in defining
possible relationships among resources.
It is a basic premise of this paper that the
assignment of metadata to resources, the
structuring of that metadata, and the relationships
among biodiversity resources expressed in their
metadata should reflect process used to collect and
create occurrence resources (i.e. the resource
creation network). Since this process is general
and applies generically to many kinds of
occurrence resources, a few general metadata
structures and relationship types (illustrated in the
RDF graphs and examples in Appendices A-B)
can be adopted rather than creating multiple
special resource classes, structures, and
relationships.
Applicability of this framework.
Significant challenges remain before the
promise of a worldwide network of biodiversity
information can come to fruition. In particular,
implementation of the GUIDs necessary for the
functioning of this network is a difficult task. It is
hoped that the framework outlined in this paper
will facilitate the development and application of
GUIDs to occurrences by clarifying what types of
resources should be identified by GUIDs and
which metadata terms can be appropriately used to
specify the properties of those resources.
ACKNOWLEDGEMENTS
I began to think about the issues raised in this
paper during an email discussion of the SERNEC
(Southeast Regional Network of Expertise and
Collections) Live Plant Imaging subgroup during
2007-08 (http://www.sernec.org/files/summary-of-
discussion.pdf). In particular, the comments of
Debbie Paul, Boyce Tankersley, Alexey Zinovjev,
and John Wieczorek were helpful in developing
my thinking as were earlier comments made by
Austin Mast. Irina Kadis provided examples in
the context of a botanical garden. Alexey
Zinovjev, Irina Kadis, John Wieczorek, and
Donald Hobern made helpful comments on drafts
of the manuscript. Two anonymous reviewers
provided useful comments and references.
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39 http://www.tdwg.org/stdtrack/article/download/150/51
40 http://www.w3.org/2001/tag/issues.html#httpRange-14
http://www2.gbif.org/GBIF-MIFTG-Report.pdf
http://www2.gbif.org/Observational_Data.pdf
http://www.tdwg.org/stdtrack/article/download/150/51
http://www.tdwg.org/stdtrack/article/download/150/51
http://www.w3.org/2001/tag/issues.html#httpRange-14
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Appendix A. Sample RDF file for the occurrence resource in Fig. 9 using the example of the
living specimen (O2) in the botanical garden scheme (Figs. 6 and 8). Other examples featuring
an image of that specimen (O4) and one of the live plant images in Fig. 6 are also provided.
The following GUIDs were used to represent resources in these examples as well as the other
appendices:
http://bigbotanicalgarden.org/individual/10224=I=tree in environment
http://saveourspecies.org/germplasm/54899= O1=seed
http://bigbotanicalgarden.org/collection/25993=O2=botanical garden specimen
http://www.ncbi.nlm.nih.gov/nuccore/BQ12345= O3=GenBank nucleotide sequence, accession number BQ12345
http://bigbotanicalgarden.org/image/52011= O4=live plant image of the living specimen.
http://stateunivherbarium.org/vascular/67988=O5=herbarium specimen
http://stateunivherbarium.org/vascular/67988#img=O6=image of herbarium specimen
http://bigbotanicalgarden.org/image/44321=live plant image of the tree in environment.
http://bigbotanicalgarden.org/ individual/10224#ABCD= D1=first determination for individual
http://bigbotanicalgarden.org/individual/10224#WXYZ= D2=second determination for individual
Note that when possible, several alternative terms from well-known vocabularies (i.e. Darwin
Core, Dublin Core, XMP, FOAF) are used to describe the same property. All of these GUIDs
are fictitious and should not be assumed to be resolvable. However, the actual RDF example
files can be downloaded by appending the file name in the example to
http://bioimages.vanderbilt.edu/rdf/examples/, e.g.
http://bioimages.vanderbilt.edu/rdf/examples/25993.rdf
----------------------------------------
Living botanical garden specimen (O2)
Contents of file http://bigbotanicalgarden.org/collection/25993.rdf containing the metadata for a
living specimen identified as http://bigbotanicalgarden.org/collection/25993
en
Living specimen of Arborus rarus
http://bigbotanicalgarden.org/collection/25993
Joe Fields
2007-09-27
false
http://bioimages.vanderbilt.edu/rdf/examples/25993.rdf
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37
41.09834
-121.17611
EPSG:4326
10
Big Botanical Garden
RDF formatted description of the living specimen
http://bigbotanicalgarden.org/collection/25993
Big Botanical Garden
2008-09-08T12:01:30-0800
en
2009-10-07T09:14:08-0800
2009-10-07T09:14:08-0800
----------------------------------------
Still image (O4) of a living specimen
Contents of file http://bigbotanicalgarden.org/image/52011.rdf containing the metadata for an
image identified as urn:lsid:bigbotanicalgarden.org:image:52011 of a living specimen identified
as http://bigbotanicalgarden.org/collection/25993
en
Living specimen image with GUID
http://bigbotanicalgarden.org/image/52011
http://bigbotanicalgarden.org/image/52011
Fred Fotografer
2009-08-03T14:24:02-0800
DigitalStillImage
false
(c) 2009 Big Botanical Garden
Big Botanical Garden
Image by Fred Fotografer, Big Botanical Garden
Living specimen of Arborus rarus in Big Botanical Garden
Available under Creative Commons Attribution-Noncommercial-Share Alike 3.0
license
http://creativecommons.org/licenses/by-nc-
sa/3.0/us/
Image of living Arborus rarus specimen (whole tree)
http://bigbotanicalgarden.org/about.htm
http://bigbotanicalgarden.org/logo.jpg
41.09834
-121.17611
EPSG:4326
10
Big Botanical Garden
Best Quality
http://www.morphbank.net/?id=987654&imgType=jpeg
image/jpeg
3456
2304
Thumbnail
http://bigbotanicalgarden.org/thumbs/52011.jpg
image/jpeg
100
67
RDF formatted description of the specimen image
http://bigbotanicalgarden.org/image/52011
Big Botanical Garden
2009-08-09T09:44:57-0800
en
2009-10-07T09:14:08-0800
2009-10-07T09:14:08-0800
----------------------------------------
Still image of a living organism in the wild (e.g. live plant image in Fig. 6)
Contents of file http://bigbotanicalgarden.org/image/44321.rdf containing the metadata for an
image identified as http://bigbotanicalgarden.org/image/44321of an individual in its environment
identified as http://bigbotanicalgarden.org/individual/10224
en
Image with GUID http://bigbotanicalgarden.org/image/44321 of individual in the
wild
http://bigbotanicalgarden.org/image/44321
Frederico Fotografo
1998-11-16T09:14:36-0300
DigitalStillImage
true
Frederico Fotografo
1998-11-16T09:14:36-0300
(c) 1998 Instituto de Plantas Nativas
Instituto de Plantas Nativas
Image by Frederico Fotografo, Instituto de Plantas
Nativas
Arborus rarus in Rio Grande do Sul, Brasil
Available under Creative Commons Attribution-Noncommercial-Share Alike 3.0
license
http://creativecommons.org/licenses/by-nc-
sa/3.0/br/
Image of living Arborus rarus specimen (whole tree)
http://bigbotanicalgarden.org/about.htm
http://bigbotanicalgarden.org/logo.jpg
-29.633905
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
41
-50.204086
EPSG:4326
10
east side of RS-484 7.9 km north of junction with BR 101
Best Quality
http://bigbotanicalgarden.org/raw-imports/dsc00234.jpg
image/jpeg
1440
2160
Thumbnail
http://bigbotanicalgarden.org/thumbs/44321.jpg
image/jpeg
67
100
RDF formatted description of the live organism image
http://bigbotanicalgarden.org/image/44321
Big Botanical Garden
1999-03-15T14:54:51-0800
en
2009-10-07T09:14:08-0800
2009-10-07T09:14:08-0800
----------------------------------------
For a functioning example of an occurrence GUID, enter
http://bioimages.vanderbilt.edu/baskauf/66921 into a web or rdf browser. Through content
negotiation, it will resolve to either http://bioimages.vanderbilt.edu/baskauf/66921.htm if
content-type text/html is requested by a web browser, or
http://bioimages.vanderbilt.edu/baskauf/66921.rdf if content-type
application/rdf+xml is requested by an RDF browser.
http://bioimages.vanderbilt.edu/baskauf/66921
http://bioimages.vanderbilt.edu/baskauf/66921.htm
http://bioimages.vanderbilt.edu/baskauf/66921.rdf
BASKAUF - ORGANIZATION OF OCCURRENCE-RELATED BIODIVERSITY RESOURCES
42
Appendix B. Sample RDF file for the resource representing an individual in Fig. 10 and the
determination resource in Fig. 11 using the example of the tree (I) and determination 2 (D2) in
the botanical garden scheme (Figs. 6 and 8). The same GUIDs were used as in Appendix A.
Contents of file http://bigbotanicalgarden.org/individual/10224.rdf containing the metadata for
an individual organism identified as http://bigbotanicalgarden.org/individual/10224 and its
determinations
en
Field individual of Arborus rarus
native
Determination of Arborus rarus var. microcarpa for the individual
http://bigbotanicalgarden.org/individual/10224
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43
Juanita Naturalista
1998-11-17
Arborus
rarus
microcarpa
variety
J. Rodriguez
Determination of Arborus rarus for the individual
http://bigbotanicalgarden.org/individual/10224
Jane Jardin
2008-06-24
Arborus
rarus
species
L.
RDF formatted description of the field individual
http://bigbotanicalgarden.org/individual/10224
Big Botanical Garden
1999-03-15T14:54:54-0800
en
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44
2009-10-07T09:14:08-0600
2009-10-07T09:14:08-0600
----------------------------------------
For a functioning example of a GUID for an individual organism, enter
http://bioimages.vanderbilt.edu/ind-baskauf/66920 into a web or rdf browser. Through content
negotiation, it will resolve to either http://bioimages.vanderbilt.edu/ind-baskauf/66920.htm if
content-type text/html is requested by a web browser, or
http://bioimages.vanderbilt.edu/baskauf/66921.rdf if content-type
application/rdf+xml is requested by an RDF browser.
http://bioimages.vanderbilt.edu/ind-baskauf/66920
http://bioimages.vanderbilt.edu/ind-baskauf/66920.htm
http://bioimages.vanderbilt.edu/baskauf/66921.rdf