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Roadmap

A summary of planned technical development of bio.tools software. The roadmap is updated in light of community input (see Contributors Guide) and on-going developments.

2018-

The discussion of new features and newly planned developments now takes place via issues: https://github.com/bio-tools/biotoolsRegistry/issues

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