figshare.md

Figshare documentation

File size

According to Figshare documentation:

All figshare.com accounts are provided with 20GB of private storage and are able to upload individual files up to 20GB.

So we don't expect files to have an individual size above 20 GB.

API

Documentation

• How to use the Figshare API
• API documentation

Token

Figshare requires a token to access its API: How to get a personnal token

Base URL

https://api.figshare.com/v2/

Query

Search guide

Rate limiting

We do not have automatic rate limiting in place for API requests. However, we do carry out monitoring to detect and mitigate abuse and prevent the platform's resources from being overused. We recommend that clients use the API responsibly and do not make more than one request per second. We reserve the right to throttle or block requests if we detect abuse.

Source: https://docs.figshare.com/#figshare_documentation_api_description_rate_limiting

Datasets

Search for MD-related datasets

• Endpoint: /articles/search
• HTTP method: POST
• Documentation: https://docs.figshare.com/#articles_search
• Documentation for search operators and searchable attributes

We search MD-related datasets by searching for file types and keywords if necessary. Keywords are searched into :title:, :description: and :keywords: text fields. Search query examples:

:extension: tpr

or

:extension: mdp AND (:title: 'md simulation' OR :description: 'md simulation' OR :keyword: 'md simulation')
:extension: mdp AND (:title: 'gromacs' OR :description: 'gromacs' OR :keyword: 'gromacs')

The POST parameters look like this:

{
    "order": "published_date",
    "search_for": ":extension: xtc",
    "page": 1,
    "page_size": 10,
    "order_direction": "desc",
    "item_type": 3
}

We search only for datasets by providing the parameter "item_type": 3.

Example of datasets related to molecular dynamics:

• Molecular dynamics of DSB in nucleosome
• a-Synuclein short MD simulations:homo-A53T
• Molecular Dynamics Protocol with Gromacs 4.0.7

Search strategy

We search for all file types and keywords. Results are paginated by batch of 100 datasets.

Get metadata for a given dataset

• Endpoint: /articles/{dataset_id}
• HTTP method: GET
• Documentation: https://docs.figshare.com/#public_article

Example dataset "Molecular dynamics of DSB in nucleosome":

• web view
• API view

All metadata related to a given dataset is provided, as well as all files metadata for this dataset.

Zip files

Zip files content is available with a preview (similar to Zenodo). The only metadata available within this preview is the file name (no file size, no md5sum).

Example dataset "Molecular Dynamics Simulations":

• The content of the file "Molecular Dynamics Simulations.zip" is available at https://figshare.com/ndownloader/files/58572346/preview/58572346/structure.json

We need to emulate a web browser to access the URLs linking to the contents of zip files. Otherwise, we get a 202 code.