þÿ

Biodiversity informatics: the challenge of linking data
and the role of shared identifiers

Roderic D. M. Page
Division of Environmental and Evolutional Biology
Institute of Biomedical and Life Sciences
University of Glasgow, Glasgow G12 8QQ, UK
r.page@bio.gla.ac.uk

Roderic D. M. Page is Professor of Taxonomy at the University of Glasgow. Perhaps
best known as the author of computer programs such as TreeView, TreeMap,
GeneTree, and COMPONENT, his recent work focuses on integrating phylogenetic,
taxonomic, and specimen databases. He is the developer of the

http://ispecies.org

search engine, and maintains a blog on phyloinformatics at

http://iphylo.blogspot.com

. From 2004 until 2007 he was editor of Systematic

Biology.

Number of words: 4974

Abstract

A major challenge facing biodiversity informatics is integrating data stored in widely
distributed databases. Initial efforts have relied on taxonomic names as the shared
identifier linking records in different databases. However, taxonomic names have
limitations as identifiers, being neither stable nor globally unique, and the pace of
molecular taxonomic and phylogenetic research means that a lot of information in
public sequence databases is not linked to formal taxonomic names. This review
explores the use of other identifiers, such as specimen codes and GenBank accession
numbers, to link otherwise disconnected facts in different databases. The structure of
these links can also be exploited using the PageRank algorithm to rank the results of
searches on biodiversity databases. The key to rich integration is a commitment to
deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and
the implementation services that link those identifiers.

Keywords: biodiversity informatics; DOI, identifiers, knowledge integration, LSID,
Semantic Web, taxonomy

Introduction

Integrating diverse sources of digital information is a major challenge facing
biodiversity informatics. Not only are we faced with numerous, disparate data
providers, each with their own specific user communities, but also the information in
which we are interested is diverse, and includes taxonomic names and concepts,
specimens in museum collections, scientific publications, genomic and phenotypic
data, and images. Of course, the problem posed by integration is not unique to
biodiversity informatics -- the wider bioinformatics community is keenly aware of
this challenge [1]. However, most bioinformatics integration efforts link together
relatively few databases built upon similar data (e.g., macromolecular sequences and
their annotations). At the time of writing the Global Biodiversity Information Facility

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 2 of 16

Page

(GBIF:

http://www.gbif.org

) lists some 214 different biodiversity data providers,

serving a total of 41,139,985 records, mostly (but not limited to) museum specimens.
The Catalogue of Life (

http://www.catalogueoflife.org

) contains over a million names

contributed by 47 sources. If we add the contents of the "traditional" bioinformatics
databases GenBank and PubMed, along with the taxonomic literature accumulated
since 1758 (much of it yet to be digitised), then the magnitude of the challenge facing
biodiversity informatics becomes readily apparent. My purpose in this review is to
outline the role that shared, globally unique identifiers [2] might play in integrating
these diverse sources of data.

Integration using taxonomic names

Integration requires shared identifiers, in other words, a way to determine whether
two items of data refer to the same entity or not. The obvious candidate for shared
identifier is the taxonomic name of an organism [3]. It is a natural link between
different databases that store information about that organism[4], and the basis of
current tools that aggregate information from multiple sources, such as iSpecies
(

http://ispecies.org

) (Figure 1).

Figure 1 iSpecies web site displaying information retrieved from separate
queries to NCBI, GBIF, Yahoo, and Google using the search term "Apomys
datae".

However, taxonomic names have serious limitations as identifiers in databases [5] as
they are not completely stable, nor are they globally unique. Names may change due
to taxonomic revision, there may be multiple names (synonyms) for the same taxon,
and the same name may refer to different taxa (homonyms).

Some of the complexities of relying on taxonomic names to links records in

different databases can be illustrated using the TbMap project [6] which links 52,778
names in the phylogenetic database TreeBASE (

http://www.treebase.org

) to names in

a number of other databases, including the NCBI Taxonomy that underlies GenBank.

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 3 of 16

Page

Less than half the names in TreeBASE correspond exactly to a name in the NCBI
Taxonomy database, and not all of those names that do match refer to the same taxon:
Loricaria in TreeBASE is a plant, whereas Loricaria in GenBank is a catfish.
Conversely, completely different names may refer to the same taxon. The plant name
Gastrolobium ebracteolatum in TreeBASE has no match in GenBank, despite the
authors listing two sequences from that plant. In GenBank the DNA sequences from
the TreeBASE study [7] (AY015102 and AY015219) are listed under the name
Oxylobium lineare. This is not an error, the two names are synonyms as a
consequence of the nomenclatural contortions forced by moving O. lineare to the
genus Gastrolobium [8].

Some of the problems encountered when using taxonomic names are a

consequence of phylogenetic research outpacing taxonomic description, hence in
sequence databases it is not uncommon to find taxa identified only to genus level or
higher (e.g., Drosophila sp.). In poorly known taxonomic groups there will be many
such taxa, consequently it may not be clear which undescribed species is being
referred to. This lack of formal names can hamper progress by leading to an unwitting
duplication of effort. As an example, three different publications on ant phylogeny in
the period 2004-2006 have each submitted a 28S rRNA sequence obtained from
specimen casent0500379 to GenBank (Figure 2), and each time the sequence has been
recorded under a different taxonomic name, namely "Proceratium sp. CS-2003-1" [9];
"Proceratium sp. 1 CSM-2006" [10]; and, "Proceratium sp. Ma02" [11]. While the
two papers published in 2006 appeared within four months of each other and so the
authors may have been unaware of each others' work, the earlier 2004 paper [9] was
cited by Moreau et al. [10].

Figure 2 Sequencing history for the ant specimen casent0500379, which was
collected in November 1998. Three 28S rRNA sequences have been obtained
from the same specimen (casent

0500379)

, published in three different papers [9-

11], and deposited in GenBank using three different names for the ant. The
sequences are placed on the timeline based on their date of submission,
publications (identified by their PubMed number) by date of publication.

While independent conformation of the sequence is comforting, this

information is attached to different taxonomic names, and hence a user extracting data
from GenBank using taxonomic names is unlikely to realize that these sequences are

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 4 of 16

Page

all from the same organism. In the same way, it will not be obvious to a user
retrieving just the 28S rRNA sequence AY325951 that additional 18S rRNA and
long-wavelength rhodopsin sequences are also available for this same specimen [10].

Figure 3 A search of GenBank for "Melissotarsus insularis" finds no sequences.
However, a search of AntWeb finds a specimen listed as having been barcoded,
and the paper publishing the barcodes has a supplementary table that lists the
specimen as the source for sequence DQ176312. GenBank lists this sequence as
being from taxon "Melissotarsus sp. BLF m1".

As a final example, consider a search in GenBank for sequences from the ant

Melissotarsus insularis. At the time of writing this search finds no sequences. We are,
however, not totally ignorant of the genome of this organism. If we search AntWeb
(

http://www.antweb.org

) we discover some 288 specimens, all from Madagascar. One

of these has the identifier casent0107663-d01, and the AntWeb record for this
specimen informs us that it has been sent to a collaborator's lab for DNA barcoding.
A literature search finds a paper on DNA barcoding ants [12] that is accompanied by
a supplementary spreadsheet of specimens sequenced, and this list includes
casent0107663-d01 as the source of GenBank sequence DQ176312. If we then go
back to GenBank and search on DQ176312, we discover it is from "Melissotarsus sp.
BLF m1" (Figure 3). The obvious implication is that what GenBank refers to as
"Melissotarsus sp. BLF m1" is Melissotarsus insularis (Figure 4), hence GenBank
does, in fact, contain information on the genome of Melissotarsus insularis.

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 5 of 16

Page

Figure 4 Linking the identifiers in Figure 3 together enables us to infer that the
taxon GenBank refers to as "Melissotarsus sp. BLF m1" is Melissotarsus
insularis.

These examples serve to illustrate two points. Firstly, databases and scientific

publications contain a snapshot of knowledge at a given time, and are not always
updated. Links between disconnected observations are made after the fact, if at all.
Secondly, the links between these disconnected observations were made using shared
identifiers such as sequence accession numbers and museum specimen codes. These
identifiers play a crucial role in bringing together seemingly unrelated data from
different sources.

Identifiers

A key prerequisite for integrating biological information from diverse sources is the
use of globally unique identifiers (GUIDs) to consistently identify objects [2]. There
are numerous schemes for generating such identifiers. Discussion within the
biodiversity informatics community has focussed primarily on three alternatives,
HTTP URIs, DOIs, and LSIDs (

http://wiki.tdwg.org/GUID

HTTP URIs

HTTP URIs (URLs) have the advantage of simplicity all a user needs is a web
browser in which to enter the URL. They are also the identifier of choice for most
Semantic Web projects [13]. Probably their greatest perceived weakness is their
fragility. Parts of a URL may reflect the technology on the web server (e.g., may
include file extensions such as ".php"), and if the web site owner changes the
software used to serve web pages, the URLs may change. The enormous freedom to
create, dispose, or reassign URLs at will has contributed greatly to the speed of
growth of the web, but as a consequence many URLs have a short life span [14].

DOIs

One approach to deploying GUIDs is to provide a central authority for assigning and
resolving identifiers. This is the strategy adopted by many academic publishers
through CrossRef (

http://www.crossref.org

) which manages Digital Object Identifiers

(DOIs) (

http://www.doi.org

) for journal articles. In some cases a field may be

dominated by a single data provider that issues de-facto GUIDs. The genomics
community uses GenBank accession numbers to identify molecular sequences, and
relies on the NCBI maintaining a stable API for retrieving information about those
sequences.

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 6 of 16

Page

Figure 5 A DOI (10.1093/bib/bbm037) and its constituent parts. This DOI
identifies reference [3].

The CrossRef model has a lot to recommend it. A DOI has two parts, the

naming authority which is assigned centrally by CrossRef (and typically corresponds
to a publisher), and the local identifier, assigned by the publisher. Because the naming
authority is assigned centrally, no two publishers will have the same naming
authority, and hence no two publishers will assign the same DOI to a different article.
The identifiers are relatively opaque, in that it is not immediately obvious which DOI
corresponds to which publisher. If one publishing company acquires another, they
will also acquire the DOIs. Given that these are not explicitly "branded" with the
name of the original publisher, they can be reused as is. Indeed, this is one of the
major attractions of DOIs in a fluid commercial landscape where publishing
companies merge or rebrand. From the user's perspective, their ability to link to a
resource is unaffected by changes in who provides that resource (note that the ability
to access the resource may well change, but it will always retain the same identifier).

But the true value of CrossRef is not in providing persistent identifiers; rather

it is the services it has built on top of those identifiers. The service most users are
familiar with is resolution: by clicking on a hyperlink in a full text article, they are
taken to the electronic version of that article. This service is provided by the Handle
technology (

http://www.handle.net

) that underlies DOIs. What CrossRef adds to the

Handle system are services, such as

· given a DOI return metadata for the corresponding article (e.g., journal and

article titles, volume, page numbers)

· given metadata for an article, return the corresponding DOI (if it exists)

The first service depends on publishers submitting metadata about each article to
CrossRef, and forms the basis for tools such as Connotea (

http://www.connotea.org

a social bookmarking service for scientists. A Connotea user need only paste in a DOI
and Connotea retrieves the metadata from CrossRef, sparing the user the need to
manually enter bibliographic details.

The second service enables the conversion of lists of literature cited in

manuscripts to lists of links to the corresponding digital resources (identifier by their
DOIs). Many publishers are now submitting lists of DOIs cited in each manuscript to
CrossRef. This enables "forward linking" the web page for an article can now
display a list of articles that cite the original article. In effect, the web page is kept
current and relevant well after its original publication.

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 7 of 16

Page

Life Science Identifiers

Life Science Identifiers (LSIDs) were developed to provide globally unique
identifiers for objects in biological databases [2]. Within mainstream bioinformatics
relatively few "early adopters" have deployed LSIDs [15], possibly in part because
core providers such as NCBI that provide stable identifiers and well documented
services have little incentive to add support for LSIDs. For the biodiversity
informatics community the attractions of LSIDs include the distributed nature of the
identifier (no central authority is required for registering or resolving identifiers), the
low cost, and the convention that resolving a LSID returns metadata in RDF. The later
facilitates integrating information from multiple sources using tools being developed
for the Semantic Web [16], although the mechanism for resolving LSIDs is not
supported by existing Semantic Web tools. LSIDs are the identifier recommend by the
Biodiversity Information Standards (TDWG) organisation (

http://www.tdwg.org

Figure 6 A LSID is prefixed with ``urn:lsid", then follows the authority,
namespace, and identifier components.

Figure 6 shows an example LSID. Each LSID is prefixed by "urn" indicating

that the LSID is a Uniform Resource name (URN), "lsid" indicates that the identifier
is resolved using the LSID protocol, then follow the authority, namespace, and
identifier components (there may also be an optional revision component to indicate
the version of the resource). The authority is a domain name that can be resolved by
the Internet DNS (typically a domain name owned by the data provider), the
namespace and identifier are specific to the data source that provides the resource. In
this example the LSID is a taxonomic name in the uBio database
(

http://www.ubio.org

). Note that the uniqueness of the LSID is in part guaranteed by

the use of Internet domain names, which are globally unique. Providing that the data
source ensures that each combination of namespace and identifier is unique within
that data source, the LSID itself will be a globally unique identifier. By using the
existing DNS infrastructure, LSIDs avoid the need to set up a new central naming
authority.

Persistence

To be useful identifiers need to be persistent, that is, users can employ them safe in
the knowledge that they won't change. Persistent identifiers are obvious candidates for
inclusion in databases. For example, a developer of a database could store an
identifier for the accepted name for each organism, and hence need to store all the
associated data about that name. Unfortunately, not all biodiversity data sources are
aware of the value of persistence. The Catalogue of Life project
(

http://www.catalogueoflife.org/)

changes identifiers with each release in 2006 the

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 8 of 16

Page

record number for the peacrab Pinnotheres pisum is 872170, whereas in the 2007
edition the record number is 3803555. Anybody populating a database with Catalogue
of Life identifiers would have to completely rebuild their database with each release.
Without a commitment to persistence it is unlikely that database developers will use
identifiers provided by other projects.

Availability

Integration based on identifiers depends on identifiers being available for the objects
of interest. At present the bulk of the records of interest to biodiversity informatics
lack identifiers. To illustrate, I extracted 9152 bibliographic citations from the
Hymenoptera Name Server database (which is dominated by papers about ant
taxonomy), and looked up each reference in CrossRef's database using their
OpenURL service. Only 251 references had DOIs, and these were concentrated in a
few journals (Figure 7). Hence the bulk of the taxonomic literature on ants lies outside
the mainstream digitally available literature. Unlike in most disciplines where the
relevance of the bulk of the literature rapidly decays with age, in biological taxonomy
publications centuries old may still be relevant, indeed vital. Hence the bias in Figure
7 towards more recently published papers is worrying.

Figure 7 Digital accessibility of literature on ants. Each point represents an
article in the Hymenoptera Name Server database. References that have DOIs
are indicated by black dots.

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 9 of 16

Page

Much of the ant literature shown in Figure 7 is accessible via URLs through

antbase (

http://www.antbase.org

), and more recently through a DSpace repository

[17] hosted at

http://plazi.org

. DSpace repositories assign Handles to objects.

Although Handles are the technology that underpins DOIs, as discussed above the
later have a much more developed infrastructure. Given any DOI, CrossRef's
OpenURL resolver provides a single place a user can go to obtain metadata about the
object, and a single place to determine whether a reference has a DOI. There are no
such services for Handles, which means their utility is limited to that of being an
identifier and little more. Given a Handle a user can retrieve a digital copy of an
article, but without knowing the specifics of the local DSpace implementation, they
cannot retrieve metadata about that article, nor can readily discover whether a given
article has a Handle.

Extracting identifiers

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 10 of 16

Page

Figure 8 Metadata in a GenBank record for the sequence AY324464 with
identifiers, or potential identifiers highlighted. In addition the sequence
accession number (a) and taxon number (d), there are text strings that can be
transformed into identifiers, such as a bibliographic citation (b) and a museum
specimen code (c).

In many cases, a database may contain records that can be converted into identifiers.
To illustrate, Figure 8 shows the metadata associated with sequence AY324463 for
the Philippine rodent Apomys datae (the subject of the iSpecies query shown in Figure
1). In addition to the NCBI identifiers of accession number and taxon number, there
are other fields that can potentially be converted into identifiers. Unlike many
GenBank records, AY324463 is not linked to a corresponding entry in the PubMed

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 11 of 16

Page

literature database. However, there are sufficient bibliographic details to use an
OpenURL [18] to find suitable identifiers. In this case CrossRef's OpenURL resolver
(

http://www.crossref.org/openurl

) returns the DOI doi:10.1111/j.1095-

8312.2003.00274.x, which identifies the publication by Steppan et al. [19]. Armed
with this identifier we can find the electronic version of this publication, view it (if we
have a subscription) or purchase it, as well as make use of any additional content
displayed by the publisher. In this case, Blackwell's list papers which cite [19], giving
us a further entry points into the scientific literature.

Similarly, the specimen voucher code has the abbreviation FMNH, which

corresponds to the Field Museum of Natural History in Chicago
(

http://www.fmnh.org

). The Field Museum's specimen records are accessible via its

DiGIR provider (

http://digir.sourceforge.net/

), and so we can retrieve details about

FMNH 167358, including the date of collection (4 April 2000) and the latitude and
longitude of the collection locality (17° 27 30''N, 121° 4' 6''E). This last piece of
information enables us to display the specimen on a map.

Palimpsest

"I likened the process of authoring a scientific paper to that of the creation
of a palimpsest. Starting from original research results and working
through the synthesis of a cogent explanation of the results or discovery,
at each step the content becomes more abstracted from the original results,
the previous work being "lost" to the reader." Leigh Dodds

Leigh Dodds' provocative blog post

(

http://www.ldodds.com/blog/archives/000264.html

) likened the process of authoring

a scientific paper to creating a palimpsest. He suggested that the underlying data
(which he equated to the underlying text, or scriptio inferior) may be more valuable
than the final manuscript (the visible content). The practice of including lists of
GenBank accession numbers and specimen codes in publications means that these
could be extracted using text-mining tools, converted into resolvable identifiers and
additional information extracted. In the Melissotarsus example presented above, it
was some metadata attached to a specimen record, together with the supplementary
material of a published paper that enabled the discovery that GenBank actually has
sequences from M. insularis. It is disconcerting, therefore, that much of this data is
consigned to the ghetto of "supplementary material" in proprietary formats such as
Excel spreadsheets or Word documents, often identified by a URL, and hence
vulnerable to loss [14].

Linking

The primary motivation for linking disparate data sources is the discovery of new
information. GenBank is primarily a database of molecular sequences, and supports
queries that reflect its origins. Users typically search for sequences that are similar to
a query sequence [20], retrieve sequences using an accession number, or browse
taxonomically. By linking sequences to georeferenced specimens (such as AY324463
to FMNH 167358) for example, one could build a view of GenBank that could be
queried geographically. Linking georeference specimens to a phylogenetic database
such as TreeBASE, one could treat TreeBASE as a biogeographic resource, rather
than simply a repository for evolutionary trees. The links also become a way of
tracing the provenance of data.

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 12 of 16

Page

But we can also exploit the structure of links themselves. A classic problem in

information retrieval is ranking the results of returned by a search engine. Algorithms
such as PageRank, [21] and Hubs and Authorities [22] compute the rank of individual
web pages as a function of incoming and outgoing links. The model of scientific
citation directly inspired PageRank; it is not just the number of times a paper is cited
but also the quality of those citations that affect the rank of a paper. The taxonomic
community has long felt disadvantaged by the perceived role of citation-based
"impact factor" in assessing the importance of taxonomic research [23], given that
much of the taxonomic literature appears in relatively low impact journals. Rather
than become embroiled in that debate, I think it more profitable to explore applying
PageRank to graphs of links between biological objects. For example, specimen
database queries may routinely return hundreds of matching records, with no obvious
criterion with which to order those results. However, if we build a graph of all the
connections between published papers, DNA sequences, images, and specimens, we
could compute the PageRank of each object and use that to rank the results.

To illustrate, AntWeb lists the 43 specimens of the ant species

Probolomyrmex tani by specimen code ordered alphabetically. This gives the user no
indication of which specimens might in some sense be more important than others. It
would be tempting to defer to criteria such as whether a specimen was a type
specimen or not, but this is a coarse criterion, and in many cases types in AntWeb are
not flagged as such. Alternatively, we could regard actions such as photographing a
specimen, extracting its DNA, or listing it in the "Material examined" section of a
paper as conferring value on a specimen, and base our ranking on those actions.

In the case Probolomyrmex tani, the holotype (casent0041505) has been

photographed (

http://www.antweb.org/specimen.do?name=casent0041505

), and three

of these images have been included in the paper describing the species [24]. The
holotype itself was also listed. We can depict these relationships using a graph where
each object is a node, and each edge in the graph represents a link between those
objects. The paper [24] is represented by a node labelled with the identifier
hdl:10199/15374 (a Handle in the Plazi repository), and there are links to the images
that comprise Figs. 1, 3, and 5 in that paper, and these in turn are linked to the
specimen they depict. There is also a direct link from the paper to the specimen,
corresponding to the specimen's presence in the list of material examined. For
comparison, a specimen not figured but simply listed (casent0009766) gets a single
incoming edge from the paper.

Another specimen listed in [24] has also been photographed, but these images

are not included that paper. However, this specimen is the source of seven DNA
sequences deposited in GenBank, and included in a phylogenetic analysis [25]. The
complete graph is shown in Figure 9, along with the PageRank scores for each node.
The specimen that has been both photographed and sequenced has the highest
PageRank, and using this criterion would appear first in the list of specimens for
Probolomyrmex tani. The graph shown in Figure 9 will grow as other data is obtained
from these specimens, but also as the two papers [24, 25] are cited. Hence, as
researchers confer value on the publications by citing them, this value will be
transmitted down the graph to the underlying sequences, images, and specimens.

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 14 of 16

Page

Closing thoughts

One could argue that of all biologists, historically it has been biodiversity researchers
have been the most aware of the need for globally unique identifiers. The
infrastructure developed to formalise taxonomic names, conventions such as
standardised abbreviations for museum collections [26], authors [27], anatomy, and
geographical place names reflect this. What is needed in the digital age is a
commitment to deploy and reuse globally unique, shared identifiers. Identifiers, by
themselves, are of little benefit without services, in particular services that link
identifiers. Given the diversity of data providers, such services will have to be able to
consume a variety of identifiers (at a minimum HTTP URIs, Handles, DOIs, and
LSIDs). A prelimary example of such a service is the bioGUID server
(

http://bioguid.info

The relatively simple infrastructure CrossRef has built upon DOIs serves as a

model of what can be achieved by adopting globally unique identifiers and basic
services. CrossRef's task is simplified by being primarily concerned with documents
of the same kind (articles, although they expanding to include images and other data),
and having a centralised infrastructure. In contrast, biodiversity data providers serve a
broad range of data types, and are not likely to be centralised. To date most
integration efforts (such as GBIF, NCBI's LinkOut, and iSpecies) rely on shared
taxonomic names to link data across multiple providers. As successful as this has
been, a richer level of integration could be obtained through shared identifiers and
services.

Key points

· Most efforts at integrating biodiversity data integration to date have relied on

taxonomic names as the shared identifier.

· Taxonomic names have limitations as identifiers, being neither stable nor

globally unique.

· A wealth of information is associated with identifiers such as GenBank

accession numbers, museum specimen codes, and bibliographic citations.

· Integrating biodiversity resources depends on using shared global identifiers,

and deploying services that link those identifiers.

· The graph of links between biodiversity data objects can be used to make new

inferences between disconnected facts in different databases. This graph can
also be used to compute the relative importance of these data objects using
tools such as PageRank.

References

Stein L. Integrating biological databases, Nature Reviews: Genetics

2003;4:337-345.
2.

Clark T, Martin S, Liefeld T. Globally distributed object identification for

biological knowledgebases, Briefings in Bioinformatics 2004;50:59-70.
3.

Sarkar NI. Biodiversity informatics: organising and linking across the

spectrum of life, Briefings in Bioinformatics 2007;8:347-357.

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008

page 15 of 16

Page

Patterson DJ, Remsen D, Marino WA et al. Taxonomic Indexing - Extending

the Role of Taxonomy, Systematic Biology 2006;55:367-373.
5.

Kennedy J, Kukla R, Paterson T. Scientific names are ambiguous as identifiers

for biological taxa: their context and definition are required for accurate data
integration. In: Ludäscher B., Raschid L. eds). Data Integration in the Life Sciences:
Second International Workshop, DILS 2005, San Diego, CA, USA, July 20-22, 2005
(Lecture Notes in Computer Science 3615). Springer Verlag, 2005, 80-95.
6.

Page RDM. TBMap: a taxonomic perspective on the phylogenetic database

TreeBASE, BMC Bioinformatics 2007;8:158.
7.

Crisp MD, Cook LG. Molecular Evidence for definition of genera in the

Oxylobium group (Fabaceae: Mirbelieae), Systematic Botany 2003;28:705-713.
8.

Chandler GT, Crisp MD, Cayzer LW et al. Monograph of Gastrolobium

(Fabaceae: Mirbelieae), Australian Systematic Botany. 2002;15:619-739.
9.

Saux C, Fisher BL, Spicer GS. Dracula ant phylogeny as inferred by nuclear

28S rDNA sequences and implications for ant systematics (Hymenoptera:
Formicidae: Amblyoponinae), Molecular Phylogenetics and Evolution 2004;33:457-
468.
10.

Moreau CS, Bell CD, Vila R et al. Phylogeny of the ants: diversification in the

age of angiosperms, Science 2006;312:101-104.
11.

Ouellette GD, Fisher BL, Girman DJ. Molecular systematics of basal

subfamilies of ants using 28S rRNA (Hymenoptera: Formicidae), Molecular
Phylogenetics and Evolution 2006;40:359-369.
12.

Smith MA, Fisher BL, Hebert PDN. DNA barcoding for effective biodiversity

assessment of a hyperdiverse arthropod group: the ants of Madagascar, Philosophical
Transactions of the Royal Society, London 2005;360:1825-1834.
13.

Sauermann L, Cyganiak R, Völkel M (2007), 'Cool URIs for the Semantic

Web', DFKI Technical Memo.
14.

Dellavalle RP, Hester EJ, Heilig LF et al. Going, going, gone: lost Internet

references, Science 2003;302:787-788.
15.

Martin S, Hohman MM, Liefeld T. The impact of Life Science Identifier on

informatics data, Drug Discovery Today 2005;10:1566-1572.
16.

Page RDM. Taxonomic names, metadata, and the Semantic Web, Biodiversity

Informatics 2006;3.
17.

Smith M. DSpace: An Open Source institutional repository for digital

material, D-Lib Magazine 2002;8.
18.

Apps A, MacIntyre R. Why OpenURL?, D-Lib Magazine 2006;12:5.

19.

Steppan SJ, Zawadzki C, Heaney LR. Molecular phylogeny of the endemic

Philippine rodent Apomys (Muridae) and the dynamics of diversification in an
oceanic archipelago, Biological Journal of the Linnean Society 2003;80:699-715.
20.

Altschul SF, Gish W, Miller W et al. Basic local alignment search tool,

Journal of Molecular Biology 1990;215:403-410.
21.

Page L, Brin S, Motwani R et al. (1998), 'The PageRank citation ranking:

bringing order to the Web', Stanford University.
22.

Kleinberg JM. Authoritative sources in a hyperlinked environment, J. ACM

1999;46:604-632.
23.

Werner YL. The case of impact factor versus taxonomy: a proposal, Journal of

Natural History 2006;40:1285 - 1286.
24.

Fisher BL. A new species of Probolomyrmex from Madagascar. In: Snelling

R. R., Fisher B. L., Ward P. S. eds). Advances in ant systematics (Hymenoptera:

Nature Precedings : hdl:10101/npre.2008.1760.1 : Posted 3 Apr 2008