D1.3 Registry Release With Comprehensive Coverage Of Elixir Node Resources, Including Resource Data Format Curation And Analysis
Creators: name: Ison, Jon
name: Ienasescu, Hans
name: Chmura, Piotr
name: Menager, Herve
name: ELIXIR Tools Community
Publisher: name: Zenodo
Year: 2018

description: The objective of EXCELERATE Deliverable 1.3 is the development of a discovery portal (bio.tools ) built upon a federated curation of a registry of key software resources for 1 bioinformatics worldwide. The core aim is to provide a practical portal that will help scientists with resource discovery and interoperability.

Four reports (D1.1 - D1.4) describe the portal:

● M12: prototyping†of portal software and registry data model, addition of seed content

● M24: consolidation†of software features and content to a stable model

● M36: expansion†of registry content towards comprehensive coverage, with new registry features

● M48: integration†with other software systems, registry applications and portalimpact evaluation

This report (D1.3 at M36) describes further consolidation†and expansion†of the registry and portal described in D1.2, which presented 5,952 bio.tools entries. We have further improved the model, ontology and software, whilst cleaning and more than doubling the registry content volume, achieving “near enough” comprehensive coverage of prevalent tools as envisioned in D1.2.

This deliverable report describes work done with ELIXIR-EXCELERATE resources.

Design and development aspects include:

● production of a major new release of the stable data model (biotoolsSchema 3.0.0) which simplifies the previous stable version 2.0 (described in D1.2) whilst extending the functionality

● the application of the “respectable beta” Tool Information Standard (see D1.5), consolidated from the prototype (see D1.2), to drive content quality improvement in bio.tools

● 3 new EDAM ontology releases

● revision of the client and server-side software including conformance to biotoolsSchema 3.0.0

Operational aspects include:

● registry growth to 11,479 entries (was 5,952 in D1.2) refactored to the model and including major clean-up and improvements guided by the Tool Information Standard

● 214,771 aggregated annotations on tools (was 97,262 in D1.2)

● content contributor growth to 800 (was 537 in D1.2), following the community build-up process (described in D1.7)

● the portal software has been made available under open license (GPL-3.0).

In addition, we describe specific developments as envisioned for milestones below (all due in M36), including new user interface features, utilities, content developments and documentation:

● M1.1.3 “EDAM release with coverage of different resource categories and RIs. Implementation of tooling for sustainable community development”

● M1.7.2 “Implementation of novel highly usable interfaces from analysis of user experience and usability requirements”

Including:

● edamBrowser web application for browsing resources (in bio.tools, TeSS etcÆ) based on their scientific (EDAM) annotation and community-development of EDAM. An article describing the work has been accepted for publication in The

Journal of Open Source Software . 2

● biotoolsSum†utility for search and browsing of local tool collections, embeddable on external Web sites

● edamMap†utility to assist curators in the creation of bio.tools entries; this text mining utility for EDAM has been improved in light of its application to bio.tools content import en masse, and is provided as a Web application and Web API We described in D1.2 how focus was shifting to content†quality†and (somewhat longer term) an increasing priority to foster the community of tool developers and tool end-users.

We also summarised an envisioned “endgame”: to provide a persistent reference to high-quality (curated and verified) “canonical” descriptions of unique†tools, with information about their provision via†online services and various downloadable artefacts, and including entries for different versions of a tool, where these have major functional differences. In this report we summarise our progress towards this endgame.

Detailed information on new, or improved technical components is available online. All aspects of the project are interdependent and work is ongoing in all areas, to drive content quality improvement, ensure sustainable growth, develop useful features for end-users and to support emerging integration scenarios and applications.