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Data management

Scratchpads data management

1 Types of supported data
Scratchpads by default are able to support a wide variety of data structures including, but not limited to:

  • Bibliographies;
  • Character projects (morphological; morphometric and molecular characters);
  • Country maps;
  • Custom content types;
  • Custom Forms;
  • Fora (with e-mail integration);
  • Images;
  • Image Galleries;
  • Taxon Pages (based on the Species Profile Model fields);
  • Taxonomies;
  • Point Localities (based on the relevant Darwin Core Fields);
  • Newsletters;
  • Basic Pages;
  • Phylogenies;
  • Polls;
  • Specimen Records (based on the relevant Darwin Core Fields);
  • Publications in Pensoft journals Note that some of these content types are available only to Scratchpads2. These content types will be extended as time and opportunity permit.

2 Data and metadata standards
Scratchpads by default support the following data standards, in which they are able to import and export data:

  • BibTeX, RIS, XML bibliographic citations (export can also be in XML, RTF or Tagged Field);
  • CSV / XLSX (spreadsheet content);
  • Darwin Core Archive and selected Extensions;
  • EXIF, XMP image metadata;
  • ITIS taxon metadata standard (for taxon names and hierarchies);
  • LUCID (for taxonomic keys);
  • Nexus (character data, export only);
  • Species Profile Model (for taxon Descriptions);
  • Structured Descriptive Data (for taxonomic keys, export only);
  • XML (export only, selected content in the TaxPub schema) http://www.ncbi.nlm.nih.gov/books/NBK47081/). Note that some of these standards are available only to Scratchpads2. These formats will be extended as time and opportunity permit.

3 Policies for access and sharing and provisions for appropriate protection/privacy
Access and sharing privileges are controlled on a page by page basis by each Site’s Maintainer. There are four pre-specified user roles that control actions through a cascading hierarchy of permissions, from Maintainer, Editor, Contributor to Anonymous User. Contributors are restricted to authoring and editing their own content, editors can author and edit any content, while maintainers also have certain administrative privileges. A click-through agreement ensures that each user agrees to a set of terms and conditions that outline their rights and responsibilities in use of the site. Each site can modify the standard Terms and Conditions as necessary, although Maintainers should note that access to personal information about individuals using the sites is covered by the UK Data Protection Act 1998 that outlines the Scratchpads administration team’s legal obligations to protect that information.
Scratchpads project administrators can gain full administrative control to any Site from a hidden account should it be necessary for maintenance purposes. We undertake that such access is done with the knowledge of the Site Maintainer.

4 Data storage, management, and backup
Data are stored across a series of Virtual Machines owned and operated by the Natural History Museum (NHM). The Scratchpads servers are backed up using IBM’s Tivoli Storage Manager that archives the last seven versions of any file contained within the system. These archives are stored on tape, and are periodically collected and stored off site, outside London. Site maintainers can request a backup of their database and site content that could be used to re-establish the Site on another server or extract and re-purpose the data. The version control system built into to the Drupal Content Management System provides full version control for content created within a site.

5 Plans for archiving and preservation of access
A mirror server run by the bioinformatics group at the Botanic Garden and Botanical Museum Berlin-Dahlem provides a synchronous copy of the Scratchpads servers. This group (part of the ViBRANT consortium) have signed a written agreement to archive, maintain and sustain access to this mirror service until 2016. The Scratchpads have been incorporated into the NHM’s digital strategy and as such are now supported by tenured staff. Whilst not guaranteeing future enhancement of the Scratchpads, it does guarantee access to the Sites for the foreseeable future.

6 How long will Scratchpads last?
The Scratchpads program was initially developed as part of the European Distributed Institute of Taxonomy (EDIT, http://www.e-taxonomy.eu/index.php), an FP6 Network of Excellence programme. It was extended by major funding through the EU FP7 research infrastructures programme (ViBRANT, http://vbrant.scratchpads.org/) and UK research council funding (e-Monocot, http://e-monocot.org/) through to December 2013. Scratchpads have seen logarithmic growth in both the number of sites and the number of registered, active users since their inception in 2007 (http://scratchpads.eu/explore). The Scratchpad code is open source (http://scratchpads.eu/develop/repository) and is being installed by various people around the world. While significant extension of Scratchpad functionality will require further grant funding, active development by other groups or individuals is already starting to appear. While we cannot guarantee that Scratchpads will exist in perpetuity the project and the data entered into Scratchpads are secure and accessible for the foreseeable future.

7 To what extent does Scratchpads record and respect licenses?
Users are encouraged to use one of the Creative Commons licences, preferably CC-BY, as described in the terms and conditions of use. Some content can be protected under an alternative licence, in mixed-mode presentation. Licences can be controlled on individual entities (i.e different on each item of content) and the provenance of all content is automatically recorded by the system. We are working toward a more granular system of attribution where metrics on the authors and up-loaders of content can be summarised and displayed. Some versions of the Scratchpads 2.0 sites (specifically the eMonocot Scratchpads profile) provide field level attribution so that multiple sources and different licences can be used for each field within a single page (node). Field-level attribution and licensing is also supported within the Darwin-Core Archive exports of these datafiles. All licences are machine readable to facilitate content sharing.

This document was last updated on 2013-05-07 15:45 (GMT+1)