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[[Image:Reference-import.png|thumb|Reference import window]]
Several '''references''' can be related to a dataset, but in principle, real ''primary data'' should be supplementary to one reference only. For information how to cite a PANGAEA dataset, see [[Citation]].
Prior to a data import, the '''reference''' related to the data has to be defined in the reference table. If a paper has a [[persistent identifier]] (DOI), it is entered in the URI-field; if no identifier exists, a link to the paper in pdf-format might be given instead (see the [[pdf]]-article on how to prepare and link pdf-files for Pangaea).  


To add a new reference in 4D, click on ''Reference'', click ''new''. As a first step (if known), you should enter:
== Definition of a reference ==
 
* [[Persistent identifier]] (DOI)  
* '''URI''': should be a [[DOI]], urn:nbn, hdl etc. or any other [[persistent identifier]]. NO links to web pages - use [[persistent identifier]] when ever available! (add the 'protocol' to the URI with ':', e.g.
* '''Author'''(s): Full names
** {{Doi|10.1016/j.margeo.2004.01.008}}
* '''Title''': full title (not abbreviated, lower case for all words but for proper nouns, no full stop at end)
** {{UrnNbn|de:0005-069975}}
* '''Source''': this field should be used for monographs, e.g.
** {{Hdl|10013/epic.10039.d001}} pdf-files can be stored in the repository [http://www.awi.de/de/infrastruktur/rechenzentrum/informationssysteme/publication_repository_epic/ ePIC] which provides a handle for persistent linking or any other repository with persistent identification.
 
You can now click on "Get Metadata" which will try to extract all of the following information from the given URI. This works with [[DOI]] Names (provided by Crossref or DataCite), some Handle types (only if provided by ePIC), but also with plain URLs to PDF/HTML/... files. For DOIs the metadata is requested from the publisher through [http://crosscite.org/cn/ web services], extracted from ePIC website, or otherwise it is extracted directly from the PDF or HTML page (title, sometimes also authors and year) using [http://tika.apache.org/ Apache TIKA] (see the webpage for all supported file formats).
 
It may happen that some of the information below needs to be completed, e.g., if the authors do not yet have entries in the [[staff]] table:
 
* '''Author'''(s): Names must already be defined in the [[staff]] table and will be added by ''multiple choice'' selection
* '''Title''': full title; no abbreviations; no full stop at end
* '''Source''': this field should be used only for any ''non-standard'' unique source information, e.g.
** Books - ''In: Bleil, U & Thiede, J (eds.), Geological History of the Polar Oceans, NATO ASI Series, Kluwer Academic Publishers, London''
** Books - ''In: Bleil, U & Thiede, J (eds.), Geological History of the Polar Oceans, NATO ASI Series, Kluwer Academic Publishers, London''
** [[Journals|grey literature]] like special reports etc.
** grey literature like special reports, etc. not published in a series
* '''[[Journal]]''': relational field to a table with 16500 most common journals
** disseration thesis, self published and issued just by the university
* '''Volume''': 53(2); set to 'submitted' or 'in press' if not yet published
* '''Journal''': full title, not abbreviated
* '''Volume''': 53(2)
* '''Pages''': 34-67 or 123 pp for complete books, thesis, reports etc.
* '''Pages''': 34-67 or 123 pp for complete books, thesis, reports etc.
* '''Year''': 1998 (for papers 'submitted' or 'in press' leave empty)
* '''Year''': publication year
* '''Status''': contains the "prepublication" status of a reference (submitted, accepted, in review, in press).
* '''Serial No''' (optional): proprietary publication number, e.g. ''AWI publ No 1234'' or ''PKDB56789''
* '''Serial No''' (optional): proprietary publication number, e.g. ''AWI publ No 1234'' or ''PKDB56789''
* '''Type''': choose as appropriate from the choice list
* '''Type''': Publication type (used internally for references formatting)
* '''Keywords''': select from [[thesaurus]] or define new as required
* '''Attachments''' (optional)
 
If using copy/paste to enter new references, avoid to add ''carriage returns'' or redundant spaces.


''In the future there will also be a service to copy/paste a full formatted citation (with or without DOI) into the reference window and look up the DOI automatically. Until this is implemented, use [http://www.crossref.org/SimpleTextQuery the simple text query interface provided by CrossRef] as a workaround.''
== Relations between a datasets and references ==


----
This describes relations between a [[Data set]] and References, which can be either external references or other datasets in PANGAEA, as well as documentation stored as attachments of references in PANGAEA's database. In the second column the [https://support.datacite.org/docs/connecting-to-works relevant Datacite relation type] is listed.
[[File:Ref-delete-requester.png|thumb|deletion requesterin references]]
Attention is required when a reference is '''deleted'''! Even if relations to data sets exist, the reference can be deleted. While pressing <Delete> the curator is prompted with a requester: ''x related records in 'DATA SET' - do you want to delete relations?'' <OK> will delete reference and relations.
----
A list of references can be '''imported''' as tab-delimited ASCII-file. A format and header tamplate is provided in the
'''[http://www.pangaea.de/curator/files/InpReference.xls '''IMPORT FORM FOR REFERENCES'''</font>]'''
by using Menue ''File/Import'', choose ''References''. Authors are also recognized by staff IDs. Author in the import list will be recognized if:
* name and first name are identical, notification if several similar names
* name and initials are identical, notification if several similar
* name identical and initial identical with initial of first name (first letters of several first names are added for comparison)
* name identical and 1. initial identical with initial of 1. first name (only if no other similar names are archived, e.g. ''Shackelton, N'' is recognized because ''Shackelton, Nicholas J''  is the only record with name ''Shackelton'' in the staff list.


For the reference management software '''EndNote X''' an export style is provided: [[Image:Pangaea2.ens.zip]].
{| class="wikitable"
----
|- style="background-color:#999;"
During data import, the relation between a data set and its reference is set. Several references can be related to a data set but in principle, real ''primary data'' should be supplementary to one reference only.
! '''PANGAEA relation type'''
----
! Datacite relation type
''Supplementary data'' should be submitted and imported ''before'' a paper is in press. After import and ''[[proofread]]'' of the data, the author is provided with a DOI for data citation/identification to be used in the publication. The paper should not just refer to the Pangaea domain, but give the link precisely pointing to the relevant data.
! Usage in PANGAEA
! Examples
|-
| '''Replaced by'''
| IsObsoletedBy
| The dataset has a new version, for example because there is an error in the previous version (note: only the new version is findable through PANGAEA search, but using the older version DOI the dataset can be still viewed).
|{{doi|10.1594/PANGAEA.947986}}
|-  
| '''New version'''
| IsPreviousVersionOf
| The dataset has a new version (note: both versions are findable).
|
|-
| '''Supplement to'''
| IsSupplementTo
| A paper and the related dataset are published at the same time, and fully referenced in both directions.<br />The dataset is published for the first time in connection with the paper.
|{{doi|10.1594/PANGAEA.922024}}
|-
| '''Related to'''
| References
| Related datasets or papers, examples of typical uses:<br />
•  Related PANGAEA datasets


Examples:
•  External datasets which are closely related, such as gene sequences (ENA)<br />
* {{doi|10.1594/PANGAEA.119754}} as a link to ''one'' specific data set or
•  Papers the data was used for, but the dataset was only published later<br />
* {{doi|10.1594/PANGAEA.472208}} as a link to a number of data sets (childs), grouped in a [[parent set]] or
•  Papers the data was used for, but not not for the first time like in supplement to<br />
* http://www.pangaea.de/search?q=@Ref896 (896 is the PANGAEA internal reference ID) to show ''many'' data sets related to a publication without a parent definition. This link may be used if many data sets (some thousand) are related to one reference.
•  Cruise reports (usually don't need to be explicitly cited, if cruise reports exist, they can be found through a pop-up window under Campaign).
|{{doi|10.1594/PANGAEA.954232}}
|-
| '''Study report'''
| IsDocumentedBy
| Used in social sciences datasets. {{doi|10.26092/elib/166}} (Handreichung)
| style="text-decoration:underline; color:#15C;" | {{doi|10.1594/PANGAEA.919342}}
|-
| '''Source'''
| IsDerivedFrom
| Typical uses:
•  When a dataset is a compilation of data from different sources, these sources can be listed under Source<br />
•  Raw dataset the processed data was derived from<br />
•  External databases that PANGAEA transferred the data from
|{{doi|10.1594/PANGAEA.932846}}
|-
| '''Previous version'''
|
| Automatic opposite relation of ''New version''
|
|-
| '''Other version'''
| IsVariantFormOf
| Connecting a dataset with a similar dataset in PANGAEA or a different repository. Typical uses:<br />• datasets with different formats (PANGAEA relational system version and a netCDF version, etc.)<br />
• datasets with different resolutions (master tracks, gridded data, etc.)<br />
|{{doi|10.1594/PANGAEA.947986}} (with external reference)
{{doi|10.1594/PANGAEA.954527}} and {{doi|10.1594/PANGAEA.954531}} (both PANGAEA)
{{doi|10.1594/PANGAEA.953085}}
|-
| '''References'''
| References
| References from Abstract, Methods or Comments relating to methodology (e.g., calculated after …, the measurement setup was described in …, the calibration equation was taken from …)
|
|-
| '''Related code / software'''
| References
| Code published elsewhere (e.g., Zenodo)
|
|-
| '''Data processing report'''
| IsDocumentedBy
| Data processing reports published at EPIC, Zenodo, sensor.awi.de or elsewhere or attached directly as pdf-file<br />
|{{doi|10.1594/PANGAEA.954531}}
|-
| '''Standard operating procedure'''
| IsDocumentedBy
| Standard operating procedures (SOP) published at EPIC, Zenodo, sensor.awi.de or elsewhere or attached directly as pdf-file
|{{doi|10.1594/PANGAEA.953085}}
|-
| '''Additional metadata'''
| HasMetadata
| Metadata details and descriptions. Typical uses:
• External: Sensor reference (laboratory or sensor record at sensor.awi.de, incl. hdl)<br />
• Attached files with additional metadata details (e.g., taxonomy, chemical compound details, etc.)
|{{doi|10.1594/PANGAEA.954014}} (Sensor.awi.de)
|-
| '''Documentation'''
| IsDocumentedBy
| Additional documentation. Typical uses:<br />• More detailed (and formatted) description of the dataset as pdf-file<br />
• Readme file
|
|-
| '''Further details'''
| IsDocumentedBy
| Typical uses:<br />• Quicklooks, overview maps and all kinds of content that doesn’t fit into any other “IsDocumentedBy” category<br />
• Station lists<br />
• Trackline maps of navigation sensors<br />
|{{doi|10.1594/PANGAEA.954531}} (station list, trackline)
|}


For refering in a publication to its primary data, the author should refer to the data by using a note like:
== See also ==
'''Supplementary data are available at {{doi|10.1594/PANGAEA.472208}}'''
* [[Data model]]


----
== Links ==
== Links ==
* [http://www.connotea.org/ Connotea] Free online reference management (provided by ''Nature'')
* [http://www.connotea.org/ Connotea] Free online reference management (provided by ''Nature'', operation stopped in 2013)
* [http://www.refbase.net refbase] Web Reference Database
* [http://www.refbase.net refbase] Web Reference Database
** example: [http://www.dfg-ozean.de/de/literatur/ Literature Database SK Ozeanographie]
** example: [http://www.dfg-ozean.de/de/literatur/ Literature Database SK Ozeanographie] (not valid anymore in 2014)
* [http://en.wikipedia.org/wiki/ISO_690 ISO standard for bibliographic referencing]
* [http://en.wikipedia.org/wiki/ISO_690 ISO standard for bibliographic referencing]

Latest revision as of 2023-01-31T13:43:24

Several references can be related to a dataset, but in principle, real primary data should be supplementary to one reference only. For information how to cite a PANGAEA dataset, see Citation.

Definition of a reference

  • Persistent identifier (DOI)
  • Author(s): Full names
  • Title: full title (not abbreviated, lower case for all words but for proper nouns, no full stop at end)
  • Source: this field should be used for monographs, e.g.
    • Books - In: Bleil, U & Thiede, J (eds.), Geological History of the Polar Oceans, NATO ASI Series, Kluwer Academic Publishers, London
    • grey literature like special reports, etc. not published in a series
    • disseration thesis, self published and issued just by the university
  • Journal: full title, not abbreviated
  • Volume: 53(2)
  • Pages: 34-67 or 123 pp for complete books, thesis, reports etc.
  • Year: publication year
  • Status: contains the "prepublication" status of a reference (submitted, accepted, in review, in press).
  • Serial No (optional): proprietary publication number, e.g. AWI publ No 1234 or PKDB56789
  • Type: Publication type (used internally for references formatting)
  • Attachments (optional)

Relations between a datasets and references

This describes relations between a Data set and References, which can be either external references or other datasets in PANGAEA, as well as documentation stored as attachments of references in PANGAEA's database. In the second column the relevant Datacite relation type is listed.

PANGAEA relation type Datacite relation type Usage in PANGAEA Examples
Replaced by IsObsoletedBy The dataset has a new version, for example because there is an error in the previous version (note: only the new version is findable through PANGAEA search, but using the older version DOI the dataset can be still viewed). doi:10.1594/PANGAEA.947986
New version IsPreviousVersionOf The dataset has a new version (note: both versions are findable).
Supplement to IsSupplementTo A paper and the related dataset are published at the same time, and fully referenced in both directions.
The dataset is published for the first time in connection with the paper. 		doi:10.1594/PANGAEA.922024
Related to References Related datasets or papers, examples of typical uses:

• Related PANGAEA datasets

• External datasets which are closely related, such as gene sequences (ENA)
• Papers the data was used for, but the dataset was only published later
• Papers the data was used for, but not not for the first time like in supplement to
• Cruise reports (usually don't need to be explicitly cited, if cruise reports exist, they can be found through a pop-up window under Campaign).

doi:10.1594/PANGAEA.954232
Study report IsDocumentedBy Used in social sciences datasets. doi:10.26092/elib/166 (Handreichung) doi:10.1594/PANGAEA.919342
Source IsDerivedFrom Typical uses:

• When a dataset is a compilation of data from different sources, these sources can be listed under Source
• Raw dataset the processed data was derived from
• External databases that PANGAEA transferred the data from

doi:10.1594/PANGAEA.932846
Previous version Automatic opposite relation of New version
Other version IsVariantFormOf Connecting a dataset with a similar dataset in PANGAEA or a different repository. Typical uses:
• datasets with different formats (PANGAEA relational system version and a netCDF version, etc.)

• datasets with different resolutions (master tracks, gridded data, etc.)

 doi:10.1594/PANGAEA.947986 (with external reference)

doi:10.1594/PANGAEA.954527 and doi:10.1594/PANGAEA.954531 (both PANGAEA) doi:10.1594/PANGAEA.953085

References References References from Abstract, Methods or Comments relating to methodology (e.g., calculated after …, the measurement setup was described in …, the calibration equation was taken from …)
Related code / software References Code published elsewhere (e.g., Zenodo)
Data processing report IsDocumentedBy Data processing reports published at EPIC, Zenodo, sensor.awi.de or elsewhere or attached directly as pdf-file
 doi:10.1594/PANGAEA.954531
Standard operating procedure IsDocumentedBy Standard operating procedures (SOP) published at EPIC, Zenodo, sensor.awi.de or elsewhere or attached directly as pdf-file doi:10.1594/PANGAEA.953085
Additional metadata HasMetadata Metadata details and descriptions. Typical uses:

• External: Sensor reference (laboratory or sensor record at sensor.awi.de, incl. hdl)
• Attached files with additional metadata details (e.g., taxonomy, chemical compound details, etc.)

doi:10.1594/PANGAEA.954014 (Sensor.awi.de)
Documentation IsDocumentedBy Additional documentation. Typical uses:
• More detailed (and formatted) description of the dataset as pdf-file

• Readme file

Further details IsDocumentedBy Typical uses:
• Quicklooks, overview maps and all kinds of content that doesn’t fit into any other “IsDocumentedBy” category

• Station lists
• Trackline maps of navigation sensors

 doi:10.1594/PANGAEA.954531 (station list, trackline)

See also

Links

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