PANGAEA Wiki - Recent changes [en]

Intern:Qualiservice Parameters

Betancort — Fri, 18 Sep 2026 08:11:11 GMT

Table: link to locations in prior residence

Intern:PANGAEA Customer Service

Cbehrens — Fri, 18 Sep 2026 05:40:36 GMT

Taxon

Awittmann — Wed, 16 Sep 2026 14:49:53 GMT

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	Taxonomic parameters are currently automatically matched with the [https://www.itis.gov ITIS] and [http://www.marinespecies.org WoRMS] taxonomic databases.		Taxonomic parameters are currently automatically matched with the [https://www.itis.gov ITIS] and [http://www.marinespecies.org WoRMS] taxonomic databases.

	Upon request and subject to available editorial capacity, PANGAEA offers the forwarding (publication) of abundance data to the Global Biodiversity Information Facility (GBIF), which integrate species occurrence records from many data providers. Other bio-geographic information systems and global portals (such as OBIS, MARBEF, etc.) rely on GBIF records for their data collections.		Upon request and subject to available editorial capacity, PANGAEA offers the forwarding (publication) of suitable abundance data to the Global Biodiversity Information Facility (GBIF), which integrate species occurrence records from many data providers. Other bio-geographic information systems and global portals (such as OBIS, MARBEF, etc.) rely on GBIF records for their data collections.

	Reference sites:		Reference sites:

Intern:Biodiversity

Pittauer — Wed, 16 Sep 2026 10:38:24 GMT

Biodiversity

Pittauer — Wed, 16 Sep 2026 10:36:39 GMT

Pittauer moved page Biodiversity to Intern:Biodiversity without leaving a redirect

New page

{{legacy}}
{{construction}}

'''Please note:''' the information on this page is heavily outdated (last edits from 2010). We are working on a rework and relaunch to provide up-to-date information. Please check our [[Biology|Best practice and templates pages for Biology]] data for the time being.

PANGAEA provides a considerable amount of '''biodiversity''' data. Beneath environmental data sets also a large number of taxon observation data is available, that is the georeferenced observation, abundance counts etc of living or dead organisms. In comparison to traditional taxonomic databases such as ITIS, PANGAEA treats this information in a slightly different way. These biodiversity databases concentrate on taxonomy issues such as taxon names, taxon author information, synonymy and classification etc., and regard this information as the ‘data’.

In contrast, PANGAEA subsumes this information within it’s metadata information and regards taxonomic information as ‘metadata’ for an underlying set of information, e.g. abundance counts. This diverging definition of data and metadata is mainly due to the fact that a considerable amount of biodiversity databases originated from collection databases where the tupel ''taxon (specimen) coordinates'' was considered as a ’record’.
==Taxonomic Information in PANGAEA==
Due to PANGAEA’s generic design the treatment of taxonomic information follows a pragmatic approach. For species occurance data taxon names are not stored in a specialiced taxonomic db structure, but within the usual ‘Parameter’ table, which documents the type of measurements or observations within a disctinct dataset. In this table taxonomic information is stored together with, other parameters, are stored for example physical parameters such as ‘Temperature’, ‘Salinity’ or complex parameters such as isotope measurements on organisms or concentrations of chemical compounds.

It was therefore important to separate and reorganize data containing taxonomic information in order to contribute taxonomic information to biodiversity portals such as GBIF or IOBIS. To ease this curatorial task, PANGAEA has developed some specialised procedures and tools to recognize taxon names. Beneath simple filters which exclude for example parameters containing special chars, PANGAEA makes also use of external services to classify parameter definitions. For example uBio’s taxonomic intelligence (http://www.ubio.org) and their public webservices to discover known taxon names. However, a considerable amount of taxon names which are used within PANGAEA have not yet been listed by the major taxonomic databases. Therefore all parameters which potentially contain taxon names are double checked by humans (data curators and librarians).

In questionable cases the responsible specialist (PI) is asked for clarification. Those parameters which certainly are recognized as taxon names are organized in dedicated taxonomic Parameter Groups. Finally, these parameters are used in a later step to transfer PANGAEA data to those standards necessary to feed the major biodiversity portals.

== Supported Biodiversity Standards ==

===Darwin Core===
The Darwin Core XML format is a simple and commonly used format to distribute biodiversity data. It is a flat XML format similar to the Dublin Core format and consists of a simple set of Core Elements it is primarily based on taxa, their occurrence in nature as documented by observations, specimens, and samples, and related information. A detailled documentation can be found at http://wiki.tdwg.org/twiki/bin/view/DarwinCore/WebHome.

PANGAEA uses Darwin Core to feed the GBIf as well as the IOBIS portal. Wheras GBIF uses the Darwin Core as specified in the above mentioned documentation, IOBIS uses a slightly different profile, which is an extension to this format. A detailled documentation of this format can be found at: http://www.iobis.org/tech/provider/schemadef1.html.

===DIGIR===
DIGIR stands for Distributed Generic Information Retrieval and is one of the most important data exchange protocols for biodiversity. As the name suggests, DiGIR was intended to provide a protocol for distributed searches allowing to formulate complex queries which are then performed on several repositories. It is therefore not ideal but also suited for data harvesting which is the primary purpose for it’s use for PANGAEA’s data submission to GBIF. A detailled documentation of DiGIR can be found here: http://digir.sourceforge.net/.

PANGAEA uses a modified PHP DiGIR provider (http://digir.net/prov/prov_manual.html) originally written by Dave Vieglais. The PANGAEA DiGIR provider can be found at http://digir.pangaea.de. This DiGIR provides biodiversity data in both, standard Darwin Core as well as IOBIS format. The transformation of PANGAEA data to fit in the structure of this provider is done by a simple script which queries the PANGAEA data base for all parameters which previously have been tagged by data curators to represent a taxon name. The data of all data sets which contain such a taxon parameter are queried and loaded into the DiGIR provider’s data base. The matrix how PANGAEA metadata and data fit into the Darwin Core model is as follows:

matrix table

The original purpose of DiGIR was to support data delivery of a distinct collection representing one dataset of biodiversity data (= DiGIR ressource). DiGIR allows to maintain more than one ressource and it allows to provide some metadata on this ressource (dataset) by a ‘Metadata Request’. This is an advantage, as the capabilities of the Darwin Core format to cite a data set are very limited. However, the response will list all metadata of any ressouce (dataset) contained. As PANGAEA provides a significantly finer granularity of data sets, we deliver a high number of data sets containing biodiversity data. Therefore, the PANGAE response to a ‘Metadata Request’ results in a very large XML file and this takes some time.

== Links ==

* parameter checker for taxa in pangaea a la Robert: http://digir.pangaea.de/checkparams.php
* [http://code.google.com/p/gbif-providertoolkit/ GBIF Provider Toolkit] better alternative

Talk:Best practice manuals and templates

Pittauer — Wed, 16 Sep 2026 10:36:01 GMT

Biodiversity Data

Pittauer — Wed, 16 Sep 2026 10:35:39 GMT

Pittauer deleted page Biodiversity Data content was: "#REDIRECT Biodiversity", and the only contributor was "Robert Huber" (talk)

Biodiversity

Pittauer — Wed, 16 Sep 2026 10:34:59 GMT

+ template construction + tepmlate legacy

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			{{legacy}}
	{{~~under~~ construction}}		{{construction}}

	'''Please note:''' the information on this page is heavily outdated (last edits from 2010). We are working on a rework and relaunch to provide up-to-date information. Please check our [[Biology\|Best practice and templates pages for Biology]] data for the time being.		'''Please note:''' the information on this page is heavily outdated (last edits from 2010). We are working on a rework and relaunch to provide up-to-date information. Please check our [[Biology\|Best practice and templates pages for Biology]] data for the time being.

Data Access and Reuse

Awittmann — Wed, 16 Sep 2026 10:24:58 GMT

removed GBIF as a service that harvests PANGAEA

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	=== External Portals and Registries ===		=== External Portals and Registries ===
	PANGAEA metadata is harvested by a large number of disciplinary and generic portals via OAI-PMH, making datasets discoverable beyond the PANGAEA website through services such as Google Dataset Search, OpenAIRE, DataCite Commons, DataONE~~, GBIF~~, EMODnet, GFBio, and others. PANGAEA is registered in re3data.org, FAIRsharing.org, RIsources, and the EOSC Marketplace.		PANGAEA metadata is harvested by a large number of disciplinary and generic portals via OAI-PMH, making datasets discoverable beyond the PANGAEA website through services such as Google Dataset Search, OpenAIRE, DataCite Commons, DataONE, EMODnet, GFBio, and others. PANGAEA is registered in re3data.org, FAIRsharing.org, RIsources, and the EOSC Marketplace.

	An alternative for search when a PANGAEA-specific search interface is not required is the '''DataCite Search API''' (https://support.datacite.org/docs/api), which searches across a large inventory of research data from many repositories. It returns summary metadata including DOI names, and subsequent data access from any PANGAEA result can then proceed via content negotiation as described below.		An alternative for search when a PANGAEA-specific search interface is not required is the '''DataCite Search API''' (https://support.datacite.org/docs/api), which searches across a large inventory of research data from many repositories. It returns summary metadata including DOI names, and subsequent data access from any PANGAEA result can then proceed via content negotiation as described below.

Intern:Qualiservice Working with the new Editorial System

Betancort — Wed, 16 Sep 2026 09:41:33 GMT

Collection Type: publication types canned responses link added

Talk:Data Rescue

Awittmann — Wed, 16 Sep 2026 08:19:29 GMT

Intern:PANGAEA Customer Service

Cbehrens — Tue, 15 Sep 2026 12:52:06 GMT

BSRN

Abuecker — Tue, 15 Sep 2026 08:05:32 GMT

Sortable Table of Stations

← Older revision		Revision as of 2026-09-15T08:05:32
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	\|https://gml.noaa.gov/grad/surfrad/dataplot.html		\|https://gml.noaa.gov/grad/surfrad/dataplot.html
	\|-		\|-
	\| Boulder \|\| BOS \|\| USA, Colorado \|\| 40.125 \|\| -105.237 \|\| 1689 \|\| 1995-07-01 \|\| LR3010 \|\| grass \|\| hilly \|\| rural \|\| \|\|BSk (Arid, steppe, cold)		\| Boulder \|\| BOS \|\| USA, Colorado \|\| 40.125 \|\| -105.237 \|\| 1689 \|\| 1995-07-01 \|\| LR3010 \|\| grass \|\| hilly \|\| rural \|\| Data collection: https://doi.pangaea.de/10.1594/PANGAEA.997370<nowiki/>\|\|BSk (Arid, steppe, cold)
	\|		\|
	\|-		\|-

Intern talk:Publication types

Pittauer — Mon, 14 Sep 2026 10:16:35 GMT

Canned responses