Web Databases and Collections

Ecological resources available on the Internet are often in databases accessed through a web interface. In this case, the concept of a page or document is less meaningful.

A single project or institution may provide access to its data or data products through a web-accessible database. For example, the University of Maryland Global Land Cover Facility provides access to remote-sensing satellite imagery, for example, net primary productivity determined using the Global Production Efficiency Model (GloPEM). Other examples include natural history museums that individually provide online access to their digitized specimen catalogs.

Digital libraries are organized collections of resources. Many of these resources historically would have been maintained on paper or film in a physical library, but modern digital libraries often include not only text or image resources but also spatial maps, software, data sets, and animations. Typically accessed through the Internet, a digital library may be aimed primarily at educators (e.g., the National Science Digital Library) or at researchers (e.g., PubMed, publications in the biomedical literature).

Registries and repositories provide access to scientific data sets and other resources from many different researchers, projects, or institutions (Table 1). A repository is an archive of data sets or resources, while a registry may not hold data sets itself but archives records describing data sets held elsewhere, that is, in a separate repository or in local databases or documents. The US National Biological Information Infrastructure (NBII) metadata clearing house is a registry largely for governmental ecological resources. Global Biodiversity Information Facility (GBIF) is an international registry for specimen-based biodiversity records. The WWW-Server for Ecological Modelling is a registry for ecological models and their documentation. By 2006, the Knowledge Network for Biocomplexity (KNB) repository included over 12 000 data sets and databases, including those of the US Long Term Ecological Research Network sites.

A data warehouse is a repository on a defined subject whose data sets share at least a core set of common fields. VegBank is an example of a data warehouse. GBIF provides tools for setting up specimen-based data warehouses.

The boundaries among these types of data-rich web-accessible resources are not distinct. While each may

Table 1 Repositories, registries, and data warehouses in widespread use within ecology. For each collection, the data standards supported are listed, and whether the collection archives the data itself

Collection name

Standards supported

Archives data

Knowledge Network for Biocomplexity

EMBL, BDP, others

Yes

NBII Metadata Clearinghouse

BDP

Noa

NSDI Metadata Clearinghouse

CSDGM

Noa

GBIF Taxonomic Collections

Darwin Core

Noa

TOPP

EML

Yes

Kruger National Park/SAEON

EML

Yes

Open Source Project for a Network

Yes

Data Access Protocol (OPeNDAP)/Integrated

Ocean Observing System (IOOS)

VegBank

US NVC

Yes

TreeBase

Yes

Storage Resource Broker

Various

Yes

ORNL DAAC

BDP, other

Yes

Global Change Master Directory

DIF

Noa

ESA Data Registry

EML

Noa

Ecological Archives (data papers)

Various

Yes

Ocean Biogeographic Information System (OBIS)

Darwin Coreb

Noa

Global Population Dynamics Database (GPDD)

Various

Yes

aAlthough this is a metadata clearinghouse, the data are often archived in other systems.

bOBIS uses an extension of Darwin Core. See Grassle FJ (2000) The Ocean Biogeographic Information System (OBIS): An on-line, worldwide atlas for accessing, modeling and mapping marine biological data in a multidimensional geographic context. Oceanography 13: 5-7. for details. BDP, Biological Data Profile; CSDGM, Content standard for digital geospatial metadata; DIF, Directory Interchange Format; EMBL, European Molecular Biological Laboratory; EML, Ecological Metadata Language; US NVC, United States National Vegetation Classification. Reproduced from Jones MB, Schildhauer MP, Reichman OJ, and Bowers S (2006) The new bioinformatics: Integrating ecological data from the gene to the biosphere. Annual Review of Ecology, Evolution, and Systematics 37: 519-544, table 1.

aAlthough this is a metadata clearinghouse, the data are often archived in other systems.

bOBIS uses an extension of Darwin Core. See Grassle FJ (2000) The Ocean Biogeographic Information System (OBIS): An on-line, worldwide atlas for accessing, modeling and mapping marine biological data in a multidimensional geographic context. Oceanography 13: 5-7. for details. BDP, Biological Data Profile; CSDGM, Content standard for digital geospatial metadata; DIF, Directory Interchange Format; EMBL, European Molecular Biological Laboratory; EML, Ecological Metadata Language; US NVC, United States National Vegetation Classification. Reproduced from Jones MB, Schildhauer MP, Reichman OJ, and Bowers S (2006) The new bioinformatics: Integrating ecological data from the gene to the biosphere. Annual Review of Ecology, Evolution, and Systematics 37: 519-544, table 1.

primarily focus on a kind of resource for a particular audience, each may also include resources of other kinds and occasionally serve audiences for which they were not originally designed.

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