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Roadmap

A summary of planned technical development of bio.tools software. Developments are informed by the ELIXIR EXCELERATE application (granted in April 2015). The roadmap is updated in light of community input (see Contributors Guide) and on-going developments. As a rule we aim for quarterly registry feature releases with supporting EDAM releases.

2017 Q3

2017 Q4

  • curation
    • planning of comprehensive coverage & systematic improvment in scientific areas via "thematic editors"
  • features / technical
    • improved search and filtering
    • drop mandatory requirement for email or URL in credits (non-breaking change in biotoolsSchema 2.1.0 and UI)
    • sorting on #citations, altmetric score, publication date etc.
    • graph of #citations, altmetric score etc. by time
    • expose publication metadata, e.g. copy-pastable citation information
    • extra enhancements to content reporting (e.g. contributors by top-level domain, contributors by geographic location, contributing institutes etc.)
    • begin implementation of integration with BioShadock, BioContainers etc. (containers), IFB cloud (VMs, workflows)
    • begin implementation of new bio.tools UI including Tool Annotator and icon-based navigation
    • begin implementation of Curator Tooling

Beyond 2017

  • features / technical
    • "tools similar to these" feature (using EDAM annotations)
    • "drive-by curation" (suggestions from non-account holders)
    • add BioSchema Tool Specification mark-up, assess impact on presentation of search results
    • provide metadata as service (tbd)
  • evaluate user impact
    • assess tool discoverability (tool cards, tool homepage URLs) via Google
  • M1.1.3 EDAM release with coverage of different resource categories and RIs. Implementation of tooling for sustainable community development
  • M1.5 Good Practice Guidelines
  • M1.6 Implementation of resource metadata catalogue & evaluation of impact of Resource Synergy Meeting series
  • M1.7.2 Implementation of novel highly usable interfaces from analysis of user experience and usability requirements
  • D1.3 Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis (Task 1)
  • D1.7 Description of the registry user helpdesk & impact on user support via community forums (Task 4)
  • D1.8 Matchmaking service: implementation & evaluation of impact
  • M1.1.4 EDAM release with coverage of different resource categories and RIs. Implementation of tooling for sustainable community development
  • D1.4 Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis (Task 1)
  • integration with DebianMed

NOTE

  • Things mentioned previously that will not be done
    • "sandbox" area for intermediate registrations. The information requirement is now lower for beta entries , "sandbox" (staging area) is not needed
    • "moderation interface" for mass content import. Instead there will be enhanced QA/QC with features for improving entries (see below)
    • improved admin interface for content management. Instead an admin will be able to edit any entry via the UI, also programmatically via Python notebooks (see below)

Changelog

A summary of technical developments of bio.tools software to date.

2017 Q2

April 2017

March 2017

  • subdomains
    • pilot for de.NBI, others
    • subdomain management in My Profile

February 2017

  • enhanced content ownership / sharing features
    • "request edit rights" button (Tool Card)
    • "request ownership" button (Tool Card, My Profile)
  • improved search

January 2017

December 2016

  • stable data model, biotoolSchema 2.0.0 released
    • defines the stable bio.tools API
    • many major changes (new credit mechanism, cleaner aggregation of links, links (including for docs and downloads) can be typed etc.
    • breaking changes reserved to once/year from now on
    • incorporates very many community requests (tracked on https://github.com/bio-tools/biotoolsSchema/issues)
    • new schema docs
  • support for candidate stable schema (Stage 1/3) in backend & user interfaces, revised documentation
  • content migration to stable schema
    • created system for semi-automated migration of content (future proofing)
    • migrated existing content (Stage 1/3), see Data model docs
  • labelling of all entries as "beta"
    • beta entries will require QC / user verification before being indexed
  • Google indexing of bio.tools
    • new indexing system (keywords and metadata representation), no longer uses prerender, Google can now index single-page applications (Javascript)
    • main site is indexed, individual Tool Cards will be indexed as we migrate from "beta" entries
  • new look Tool Cards
  • bio.tools updated for EDAM_16
  • support for EDAM synonyms for registration via API

November 2016

  • revised https://bio.tools/stats pages with new graphs, cleaner look and feel etc.
  • revised search mechanism, now performs exact and fuzzy searches
  • revised Registration Interface, now provides inline error reporting
  • feature to send verification (for account creation) and password reset emails
  • features to share resources moved to "my profile" page
  • scheduling system for housekeeping, e.g. gathering stats for https://bio.tools/stats
  • misc. bug fixes

October 2016

  • moved dev.bio.tools into production (consolidation of dev.bio.tools & bio.tools content) with QC check for redundant tool names
  • content ownership / sharing of edit rights (Google docs style)
    • ownership is not based on affiliation anymore, 1 owner / tool, edit rights can be shared with selected account holder, or with all account holders
  • stable tool ID / URL scheme including tool version number
    • moved away from affiliation-name-version triplet for identifying entries, tools now identified by toolID, specific versions of a tool identified by versionID. IDs have syntax constraints (defined in https://github.com/bio-tools/biotoolsSchema/).
    • IDs and therefore Tool Card URLs will be user-verifiable (implementation tbd)
  • improved bio.tools auto-mailer (using admin email address)
  • added historical stats to bio.tools/stats

July 2016

  • rewrite bio.tools software to pay off technical debt (completed)

June 2016

  • ~750 automated unit tests
  • new and improved grid view
  • "my profile" page, with account information and list of tools registered by this account
  • Curation admin interface (content edition) (beta)
  • General admin interface (account management, password change, reset etc) (beta)

May 2016

  • robust validation of incoming tool descriptions
  • new URL / persistent ID scheme
  • unit tests for EDAM topics, operations, data types and formats

April 2016

  • bio.tools/stats page
  • improved load time
  • added Elasticsearch support for improved search
  • user authentication support for password change, reset, etc
  • new improved and simplified search and filtering interface (neXtProt style)

March 2016

December 2015

  • Created URL links to various registry related resources, such as bio.tools/events
  • Displaying date added as 'time ago'
  • Improvements to the pagination
  • Added a nightly validator that ensures that the existing contents of the registry validate against the XSD schema
  • EDAM release
  • Continuous debugging and improvements

November 2015

  • Created a mechanism for gathering stats of the current content of the registry
  • API now returns date of last update
  • Sorting entries by last added
  • Improvements to the account creation
  • Schema release
  • Continuous debugging and improvements

October 2015

  • Rework of all interfaces to make website mobile friendly
  • Improved error handling, messages and display when registering a resource
  • Made JSON interactively editable in the ¡®Resource registration¡¯ interface
  • Continuous debugging and improvements

September 2015

  • New domain bio.tools
  • New advanced filtering widget and mechanism
  • Improvements to the EDAM widget
  • Tooltips redone
  • Updated the contact tab in ¡®Resource registration¡¯ to make it obvious that either email or URL is required instead of both
  • Continuous debugging and improvements

August 2015

  • Major release with focus on improved interface usability: - Removed splashscreen - Refactored menus - New browsing interface: added new ¡®pill¡¯ view, new sorting capabilities, storing search state in the URL etc. - New registration interface: new ontology browsing widget, restructured to improve look and feel - New editing interface (for existing resources) - Added ¡®compact view¡¯ to query interface - Improved search bar with search suggestions
  • Finalizing search API intended to prepare for growth in content and usage of the registry (scalability)
  • New transferable search URL - same syntax for filtering both via GUI and API
  • Continuous debugging and improvements

July 2015

  • Work on a search API intended to prepare for growth in content and usage of the registry (scalability)
  • Implemented Resource Pages (mature) - New look: compactified, visualisation of functions and in/outputs
  • Work on major enhancements to interface usability
  • Continuous debugging and improvements

June 2015

May 2015

  • Created new demo server
  • Created replacement page for use upon releases
  • Set up Google Indexing
  • Enabled Google Analytics
  • Implemented Resource Pages (beta)
  • Made publication attribute mandatory
  • Created biotoolsXSD project in Github
  • biotoolsXSD-1.1 released - https://github.com/jongithub/biotoolsxsd/blob/master/CHANGELOG.md - Updated schema docs for "Name" standards - Updated schema docs to include simple table of attributes (optional, recommended, mandatory) PLUS reference Google Doc with this info
  • Continuous debugging

April 2015

  • Added ability to adjust column width
  • Added ability to sort columns
  • Outlined technical implementation of Resource Pages
  • Enforced "name" standards in registration interface
  • Prepare for Google Indexing
  • Added whole VM deployment and provisioning setup
  • Various schema updates, e.g. - Improved dataType, dataFormat element docs - Extended URL with support for FTP - Enforced ¡®description' length limit - Enforced other 'description' fields¡¯ length limits - Made publication ID mandatory - Updated sample JSON with "null" value of "uri"
  • Continuous debugging

March 2015

  • Batch registration to support XML format, & support multi-resource JSON / XML upload
  • Fixed the interface not to direct the user to the splash screen all the time
  • Various schema updates, e.g. - Harmonize "Maturity" in software description schema - Updated comment in schema docs for "contact" - Removed URI from softwareType and resourceType - Updated schema for missing AppDB languages - Updated schema for missing AppDB licenses
  • Continuous debugging

February 2015

  • Released EDAM 1.9 with corresponding registry updates
  • Splash page updated to accept full term before redirecting
  • Various schema updates, e.g. - Added "virtual appliance" to enum for interfaceType - Removed URLs from simple enums in schema (old SWO terms) - Changed "Accessibility" element to support "private" tools - Added "Dataset" to enum for resourceType
  • Continuous debugging