Difference between revisions of "Technical documentation of PANGAEA management software"
Robert Huber (Talk | contribs) |
|||
| (15 intermediate revisions by 5 users not shown) | |||
| Line 1: | Line 1: | ||
| + | == 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" | {| class="wikitable" | ||
! style="font-weight: bold;" | | ! style="font-weight: bold;" | | ||
! style="font-weight: bold;" | Database,system, Homepage | ! style="font-weight: bold;" | Database,system, Homepage | ||
| − | ! | + | ! https://www.pangaea.de |
|- | |- | ||
| rowspan="5" style="font-weight: bold;" | General Information | | rowspan="5" style="font-weight: bold;" | General Information | ||
| Line 9: | Line 17: | ||
|- | |- | ||
| style="font-weight: bold;" | Contact persons | | style="font-weight: bold;" | Contact persons | ||
| − | | M. Diepenbroek, R. Huber, J.Felden | + | | M. Diepenbroek, R. Huber, J. Felden, J. Weber |
|- | |- | ||
| style="font-weight: bold;" | Developer group, country | | style="font-weight: bold;" | Developer group, country | ||
| − | | PANGAEA IT staff at MARUM : M. Diepenbroek & U. Schindler | + | | PANGAEA IT staff at MARUM: M. Diepenbroek & U. Schindler |
|- | |- | ||
| style="font-weight: bold;" | Data domains | | 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 | | style="font-weight: bold;" | Organismic data | ||
| Line 25: | Line 33: | ||
|- | |- | ||
| style="font-weight: bold;" | User rights management | | style="font-weight: bold;" | User rights management | ||
| − | | Database: | + | | Database: PostgreSQL; Editorial system: internal |
|- | |- | ||
| style="font-weight: bold;" | Client | | style="font-weight: bold;" | Client | ||
| Line 64: | Line 72: | ||
|- | |- | ||
| style="font-weight: bold;" | Training | | style="font-weight: bold;" | Training | ||
| − | | Data curator training by PANGAEA staff at AWI | + | | Data curator training by PANGAEA staff at AWI and MARUM |
|- | |- | ||
| style="font-weight: bold;" | Notes | | style="font-weight: bold;" | Notes | ||
| Line 83: | Line 91: | ||
|- | |- | ||
| style="font-weight: bold;" | xml according EML schema | | style="font-weight: bold;" | xml according EML schema | ||
| − | | | + | | as part of DwC archives |
|- | |- | ||
| style="font-weight: bold;" | xml according other schemas | | style="font-weight: bold;" | xml according other schemas | ||
| Line 89: | Line 97: | ||
|- | |- | ||
| style="font-weight: bold;" | txt, CSV export | | style="font-weight: bold;" | txt, CSV export | ||
| − | | yes | + | | yes, DwC Archives |
|- | |- | ||
| style="font-weight: bold;" | Notes | | 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]] | ||
| + | |||
| + | |||
| + | ---- | ||
| + | |||
| + | Status: August 2021 | ||
| + | ---- | ||
| + | |||
| + | Back to [[Technical Documentations]] | ||
| + | |||
| + | [[Category:Technical Documentation of software used by GFBio Partners]] | ||
Latest revision as of 15:35, 2 August 2021
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
| Database,system, Homepage | https://www.pangaea.de | |
|---|---|---|
| General Information | Installations at GFBio collection data centers/ archives | |
| Contact persons | M. Diepenbroek, R. Huber, J. Felden, J. Weber | |
| Developer group, country | PANGAEA IT staff at MARUM: M. Diepenbroek & U. Schindler | |
| 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. | |
| Organismic data | all recent and fossil organisms groups | |
| Software and Database System | Operating System Server | UNIX |
| User rights management | Database: PostgreSQL; Editorial system: internal | |
| Client | 4D PANGAEA Editorial system; PANGAEA web frontends | |
| GIS functionalities | Gmap | |
| GUIs for data import | 4D PANGAEA Editorial system; Bulk upload via import sheets, txt, csv | |
| GUIs for data export/ reports | Dataset level: PANGAEA web frontend, HTTP download in various formats; Bulk/mass download: PANGAEA data warehouse | |
| GUI language | default: english | |
| Open access | yes | |
| Open source | no | |
| Licenses | creative commons | |
| Information model online | http://wiki.pangaea.de/wiki/Data_model | |
| State of development | stable | |
| Code,language, developer platform | Java, C, PHP & Javascript | |
| User manual | http://wiki.pangaea.de/wiki/Main_Page | |
| Training | Data curator training by PANGAEA staff at AWI and MARUM | |
| Notes | ||
| Interfaces to export data in various schemas and standards | xml according ABCD schema | no |
| BioCASe Wrapper Version installed, description of dataflow | no | |
| xml according DarwinCore schema | yes | |
| xml according EML schema | as part of DwC archives | |
| xml according other schemas | ISO19136, DIF, Dublin Core,etc.. | |
| txt, CSV export | yes, DwC Archives | |
| Notes | community driven export scripts using PANGAEA APIs: https://github.com/ropensci/pangaear
Python library: |
GFBio Integration
Submission and Ingestion of Data
Data providers submit their original research data and corresponding metadata via the 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 [PANGAEA standard data curation and archiving process] guided by dedicated data curators.
Status: August 2021
Back to Technical Documentations
