View source for Technical documentation of PANGAEA management software

== PANGAEA ==
PANGAEA is a globally leading information system, long term archive and data publisher for geoscientific, biological and environmental data. 
Jointly hosted by the Centre for Marine Environmental Sciences (MARUM) at the Universität Bremen and the Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), PANGAEA is laid out as a permanent facility, guaranteeing the long-term availability and accessibility of archived data and metadata in secure and machine readable formats. Data published by PANGAEA origins from a broad range of subdisciplines of the  Biological Sciences, Chemistry, Physics with a special focus an Earth Sciences and Environmental Sciences.
It is World Data Center (WDC-PANGAEA) accredited by the International Council for Science (ICSU)  World Data System. Further, it holds mandates from the World  Meteorological Organization (WMO) as a World Radiation Monitoring Center (WRMC). Archiving follows the Recommendations of the Commission on Professional Self Regulation in Science for safeguarding good scientific practice and the Organisation for Economic Co-operation and Development (OECD) Principles and Guidelines for Access to Research Data from Public Funding. 
PANGAEA is the designated archive for the journal Earth System Science Data (ESSD) and recommended data repository of several international scientific journals such as “Scientific Data” by the Nature publishing group. 
Essential services supplied by PANGAEA are data curation, long-term data archiving and data publication. Data curation includes quality control of metadata and the development of ontologies and vocabularies according to international protocols and standards. Metadata are extensive and each dataset can be cited using a universally unique Digital Object Identifier (DOI). The system is operated in the sense of the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities which is a follow up to the Budapest Open Access Initiative.

==Documentation==
{| class="wikitable"
! style="font-weight: bold;" | 
! style="font-weight: bold;" | Database,system, Homepage
! https://www.pangaea.de
|-
| rowspan="5" style="font-weight: bold;" | General Information
| style="font-weight: bold;" | Installations  at GFBio collection data centers/ archives
| 
|-
| style="font-weight: bold;" | Contact  persons
| M.  Diepenbroek, R. Huber, J. Felden, J. Weber
|-
| style="font-weight: bold;" | Developer  group, country
| PANGAEA  IT staff at MARUM: M. Diepenbroek & U. Schindler
|-
| style="font-weight: bold;" | Data  domains
| Data published by PANGAEA origins from a broad range of subdisciplines of the Biological Sciences, Chemistry, Physics with a special focus an Earth Sciences and Environmental Sciences.
|-
| style="font-weight: bold;" | Organismic  data
| all  recent and fossil organisms groups
|-
| rowspan="17" style="font-weight: bold;" | Software and Database System
| style="font-weight: bold;" | Operating  System Server
| UNIX
|-
| style="font-weight: bold;" | User  rights management
| Database:  PostgreSQL; Editorial system: internal
|-
| style="font-weight: bold;" | Client 
| 4D  PANGAEA Editorial system; PANGAEA web frontends
|-
| style="font-weight: bold;" | GIS  functionalities
| Gmap
|-
| style="font-weight: bold;" | GUIs for  data import
| 4D  PANGAEA Editorial system; Bulk upload via import sheets, txt, csv
|-
| style="font-weight: bold;" | GUIs for  data export/ reports
| Dataset  level: PANGAEA web frontend, HTTP download in various formats; Bulk/mass  download: PANGAEA data warehouse
|-
| style="font-weight: bold;" | GUI  language
| default:  english 
|-
| style="font-weight: bold;" | Open  access
| yes
|-
| style="font-weight: bold;" | Open  source
| no
|-
| style="font-weight: bold;" | Licenses
| creative commons
|-
| style="font-weight: bold;" | Information  model online
| http://wiki.pangaea.de/wiki/Data_model
|-
| style="font-weight: bold;" | State of  development
| stable
|-
| style="font-weight: bold;" | Code,language, developer platform
| Java, C,  PHP & Javascript
|-
| style="font-weight: bold;" | User  manual
| http://wiki.pangaea.de/wiki/Main_Page
|-
| style="font-weight: bold;" | Training
| Data curator  training by PANGAEA staff at AWI and MARUM
|-
| style="font-weight: bold;" | Notes
| 
|-
| style="font-weight: bold;" | 
| 
|-
| rowspan="7" style="font-weight: bold;" | Interfaces to export data in various schemas and  standards
| style="font-weight: bold;" | xml  according ABCD schema
| no
|-
| style="font-weight: bold;" | BioCASe  Wrapper Version installed, description of dataflow
| no
|-
| style="font-weight: bold;" | xml  according DarwinCore schema
| yes
|-
| style="font-weight: bold;" | xml  according EML schema
| as part of DwC archives
|-
| style="font-weight: bold;" | xml  according other schemas
| ISO19136,  DIF, Dublin Core,etc..
|-
| style="font-weight: bold;" | txt, CSV  export
| yes, DwC Archives
|-
| style="font-weight: bold;" | Notes
| community driven export scripts using PANGAEA APIs: https://github.com/ropensci/pangaear
Python library: 

https://github.com/pangaea-data-publisher/pangaeapy
|}

== GFBio Integration ==

=== Submission and Ingestion of Data ===

Data providers submit their original research data and corresponding metadata via the [https://submissions.gfbio.org/ GFBio Submission System] to PANGAEA.
The submission systems uses the GFBio Submission Brokerage System to trigger a data submission event via the PANGAEA internal ticket system. Each data submission is handled according to the [[https://wiki.pangaea.de/wiki/Data_submission PANGAEA standard data curation and archiving process]] guided by dedicated data curators.

[[File:PANGAEA GFBio.png|400px|PANGAEA GFBio workflow]]


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Status: August 2021
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[[Category:Technical Documentation of software used by GFBio Partners]]