Welcome in MetaShARK
DISCLAIMER: some features are still in development. Some parts with this color code are not meant to be fully functional.
MetaShARK
MetaShARK (Metadata Shiny Automated Resources and Knowledge) is a tool designed for ecology data description tasks. The tool relies on ecology metadata standards, and mainly the Ecological Metadata Language. Its vocation is to allow any ecologist to fill in metadata for its dataset to permit the understanding, resusability and reproducibility of his work. But as metadata is becoming more and more complex, this tool is trying to get as user-friendly as possible.
MetaShARK
is written and maintained by the French
National Biodiversity Data Hub (PNDB). You can interact with the
development team on their
git repository.
EML
The Ecological Metadata Language has been developped since 1997 from the work of Michener et al.. Since then, it has been developped by the NCEAS (National Center for Ecological Analysis and Synthesis) and is mainly accessible through its github repository. However, MetaShARK offers a documentation section dedicated to EML. Since the 2.2.0 release, EML published an online documentation, accessible from the Documentation tab.
MetaCat & MetaShark
The application you are currently using is a front-end tool for any user who wants to contribute to a DataOne node repository, also known as metadata catalogue or MetaCat. To contribute to a MetaCat, you need to login to the metacat in which you want to upload your data package. Then, it will be possible for MetaShARK to gather the needed informations, as you will see while using the app. The upload feature is accessible from the Upload tab. It will require to have a written EML file available in this instance of MetaShARK.
About EML Assembly Line
Authorship
The
EML Assembly Line
package used in this app and its
children is the intellectual property of the Environment Data
Initiative (EDI). You can find further details on their
git repository
Usage
EMLassemblyline is a metadata builder for scientists and data managers who need to easily create high quality EML metadata for data publication. It emphasizes auto-extraction of metadata, appends value added content, and accepts user supplied inputs through template files thereby minimizing user effort while maximizing the potential of future data discovery and reuse. EMLassemblyline requires no familiarity with EML, is great for managing 10-100s of data packages, accepts all data formats, and supports complex and fully reproducible science workflows. Furthermore, it incorporates EML best practices, is based on a simple file organization scheme, and is not tied to a specific data repository.
(preface by Colin Smith, EDI)|
|
Welcome in the EML Assembly line. This tool is basically designed as a package, embedded in Shiny within MetaShARK. This little helper aims to show you what awaits you in the further steps.
After loading/creating a data package, a navigation bar will appear on your right. There features the following buttons:
- Quit: click this to leave the edition of the current data package. You will be asked if you wanted to save the current changes. You can switch to other section of the app (e.g. documentation) without losing the current metadata.
- Save: click this to save the current changes in the filled metadata. This will write a save file in the data package directory. Then, metadata will only be lost with data package removal.
- Next: click this to continue your metadata filling. It will bring you to the next step.
- Previous: click this to come back to the previous step.
Edit existing data package
If you have handled manually some packages in
~/dataPackagesOutput/emlassemblyline
, some packages might not be listed here.
Create new data package
Only use alphanumerics, or one of:
. , : _ -
CC0: public domain.
CC-BY-4.0: open source with authorship.
For more details, visit Creative Commons.
- Until now, only table files are supported.
- Selecting a file will immediately upload it (heavy files might be slow).
- Editing a data file requires removing it and uploading its newest version.
Even if EML Assembly Line automatically infers most of your data's metadata, some steps need you to check out. Please check the following attribute, and fill the required fields. Once they will be filled, corresponding fields will turn to green.
Attributes list
Attribute description
Custom units
Variables list
You can fill in geographic coverage through two methods: either by chosing variables from your files, or manually define it. Mixed approach is not supported. Check the help above for more details. Only WGS84 is currently supported.
columnsMethod
DISCLAIMER
- Unsupported special characters, symbols, formatting, or hyperlinks (URLs are acceptable).
- Any file selected will not be overwritten but will be used to fill in content (except files originating from Data Package itself).
Organize your keywords in keyword sets. You can assign a keyword thesaurus (controlled vocabulary or ontology) for each of your keyword set. Press RETURN to input a keyword.
If you have additional information that doesn't fall under the scope of the abstract or methods (e.g. a list of research articles or thesis derived from this dataset) about your dataset, you may share it here.
We're almost there !
By clicking this button, you will process your metadata into a EML-valid xml file. Please note that you will be able to edit this data package furtherly.
In case of error, please click here to report any bug. (github login required)
Publish data package
You can head to the Upload tab and publish your data package to a metacat repository.Download your data package
Get a local version containing MetaShARK files, EML Assembly Lines templates and the written metadata at xml format. Compressed in a zip archive.MetaFIN: WIP
Select your MetaCat portal
dev
portals are under construction. No guarantee
is given of their consistance.
prod
portals are
completely functional. Chosing 'Other' will ask you to input some
technical information.
Want your endpoint to be listed? get in touch with the dev team !
Get your authentication token
The authentication token is a user-specific characters key. It allows the user to authenticate a connection between its current location and a distant server, actually the metadata catalog. To upload a data package, the authentication token is required.
Action to perform
Please point out whether this data package was never published (prime upload) or this is meant to be updated (update). If you are updating your data package, you will be asked to identify the previous version of the data package.
Select your data package files
You can either select a data package from ~/dataPackagesOutput/emlAssemblyLine/ or pick up the files one by one. Selecting a data package will erase any previous selection.
Select a data package
Add or remove files
Files list
About MetaShARK dev team
MetaShARK is developped within the french Museum National d'Histoire Naturelle / UMS Patrimoine Naturel / Pole National de Biodiversite. Its development team is currently composed of Elie Arnaud (lead developer) and Yvan Le Bras (team director).Thanks
MetaShARK could not be built without the help of those people:- Colin Smith (EDI, US) who collaborates with us since March 2019, and currently provides us the EML Assembly Line tool.
References
LTER and EML Actors
The following people and parties have worked upstream of MetaShARK dev team to provide the fundamentals united in the present tool.
Computer material
The following references will lead the user to the source of tools and methods reused in MetaShARK.
Literature
MetaShARK is based on the following papers and articles concerning mainly ecological metadata.