3DBIONOTES

1. Resource facilitation to scientific research

a. Interoperability Resource: Briefly describe the function of the Interoperability Resource

3DBIONOTES is a web platform that defines a common interface to explore the different levels of molecular biology including structural, genomic, proteomic and interactomic data, into a very interactive graphical environment. The system core integrates most relevant bioinformatics databases including UniProt, ENSEMBL, wwPDB and EMDB into a unique framework that provides an integrated management of these resources. The system is enriched with biomedical and biochemical information that annotates the core databases and are displayed over the different molecular levels. Current annotation sources include: posttranslational modifications, genomic variants and diseases, disorder, epitopes, protein domains and others.

b. Scope statement: describe the scope , and the users of the resource. How is the Interoperability Resource positioned with respect to other similar Interoperability Resources ? Include the base URL and, if relevant, the introductory or “about” page URL.

3DBIONOTES provides a graphical environment to explore biological annotations on protein structures and thus, has a clear impact on the structure biology scope and in particular in those research projects that aims to solve novel structures of protein complexes. However, the application can be also useful in a broad range of molecular biology areas where protein knowledge plays a central role as studies on protein function or protein-protein interactions. Moreover, the application supports the analysis of multiple proteins and thus, it can be used to explore protein interaction networks. In this way, 3DBIONOTES can be used for the analysis of biological annotations on protein complexes and protein interactomic networks.
3DBIONOTES API can be used for submitting structural models and external sets of annotations in such a way that can visualise other application results. Then, 3DBIONOTES can become an online visualisation tool for applications that computes structural models as protein docking, homology modelling or protein folding. In the same way, the application can display computed or predicted features of protein sequences or structures from external applications and thus, can be used as a viewer to display the predicted annotations with the different sources of information already included in the framework. Moreover, the API also provides different methods to directly retrieve biological annotations from the integrated sources and the alignments or mappings between the core databases, i.e. genes, protein sequences and structures. Then, 3DBIONOTES can be useful in any bioinformatics project were mappings between protein and gene coordinates are needed.

c. Resource url

https://3dbionotes.cnb.csic.es

d. Inter-organisational recognition: does the Interoperability Resource have community recognition? (e.g. demonstrated through a collaboration, geographical diversity in the source of the submissions, international diversity of delivery partners and/or funders)

3DBIONOTES is being used by several well-known applications and databases to visualise their entries and computed results. Most important databases of cryoEM maps, EMDB EU and EMDB US use 3DBIONOTES as a visualisation tool for their structures and all of their entries are linked to 3DBIONOTES web application. HADDOCK web server, an online application for computing protein docking, uses 3DBIONOTES to display the structure of the predicted complexes, in this way HADDOCK users can display their docking results in the enriched 3DBIONOTES environment including all biological annotation sources. Finally, PDB-REDO database, a repository of optimised crystallographic structure models, links its entries to 3DBIONOTES to display the refined structures.

3DBIONOTES is being developed in the context of ELIXIR as part of the ELIXIR-ES node projects and its development was supported by the Spanish health system institute Carlos III. Moreover, the application is also one of the bioinformatics services in the WestLife project, that is comprised by 10 partners (10 partners, STFC (UK), Instruct, NKI (NL), LUNA (FR), UU (NL), CIRMMP (IT), INFN (IT), EMBL, MU (CZ), CSIC (ES)) that provides computational services for structural biology, and it is being used by other WestLife tools for result visualisation.

The number of accessions to 3DBIONOTES have been tracked using google analytics since March 2017 and more than different 2700 users involving over 70 different countries from all continents have accessed the application.

2. Community

a. Community impact: If applicable, provide documented evidence of community impact (e.g., publication citations, API calls, projects using the resource, etc.)

Citations: 8

Uses from March 2017
• Users: 2.760
• Accessions: 11.548

Current projects using 3DBIONOTES for data visualisation:
• EMDB Europe https://www.ebi.ac.uk/pdbe/emdb/
• EMDB US http://www.emdatabank.org/
• HADDOCK webserver http://milou.science.uu.nl/services/HADDOCK2.2/haddock.php
• PDB_REDO webserver https://pdb-redo.eu/

b. Potential usage: Describe other systems that could use this candidate resource, but currently do not.

In general, any application or database that handles protein structural models and/or protein features are potential users of 3DBIONOTES.

Databases that could use 3DBIONOTES:
• PDBe EU https://www.ebi.ac.uk/pdbe/ 
• RCSB US https://www.rcsb.org 
• UniProt https://www.uniprot.org 

Applications that could use 3DBIONOTES:
• Phye2 http://www.sbg.bio.ic.ac.uk/~phyre2
• SiteBinder2 https://webchem.ncbr.muni.cz/Platform/App/SiteBinder
• Swiss-Model https://swissmodel.expasy.org/
• HotSpotWizard https://loschmidt.chemi.muni.cz/hotspotwizard/

c. Outreach & support: Provide resource support publication(s)/user documentation(s) describing the Interoperability Resource (e.g. scientific journal publications, community preprints, resource user’s documentations etc.), resource dissemination plan (e.g. workshops, conference presentations), and other equal-opportunity research support (if applicable).

Publications:
• Tabas-Madrid, D., et al. 3DBIONOTES: A unified, enriched and interactive view of macromolecular information. J Struct Biol 2016;194(2):231-234.
• Segura, J., et al. 3DBIONOTES-WS: A web server for the automatic annotation of macromolecular structures. Bioinformatics. 2017 Nov 15;33(22):3655-3657

Conferences:
• Basel Computational Biology Conference ([BC]2). Basel, Switzerland. September 2017. (POSTER)
• Structural Bioinformatics & computational biophysics (3DSIG – ISMB/ECCB). Prague, Czech Republic. July 2017. (POSTER) 
• BIOTEC2017. Murcia, Spain. June 2017. (ORAL PRESENTATION)
• 15th European Conference on Computational Biology. The Hague, Netherlands. September 2016. (POSTER)

3DBIONOTES will be presented at the upcoming ECCB 2018 in the ELIXiR tracks.

d. Dependency of other resources: How is this resource critical to the user(s)? Do other resources depend on the resource described here to provide downstream service? Please list, or provide a link to a diagram.

Currently 3DBIONOTES is being used by EMDB EU and US repositories, HADOCK web server and PDB-REDO databases as a 3D viewer in their web sites. Although, the application itself is not central in their execution workflows, it provides a very helpful view of their data and computed results. Indeed, more than 5000 requests were processed from their websites during last year.

3. Quality of resource

a. Uptime: Average percentage uptime/month during the last 12 months, response time of the resource. In case of ontology/standards production, interval of update/release, adaptability of ontology design patterns to evolving data. Provide information where applicable: uptime of resource, software release cycle (please state week/month etc), update frequency.

The production server has been active more than 99% during last 12 months. Core databases are updated weekly while biological annotations are updated monthly.

Entry at OpenEBench:
https://openebench.bsc.es/html/#!/tool/3dbionotes 

Entry at bio.tools:
https://bio.tools/3dbionotes 

b. Accessibility: what are resource retrieval mechanisms? Does the resource provide web-based user interface, application programmable interface (API), containers, and/or other channels? Please list resource access mechanism, provide URLs as applicable.

3DBIONOTES web application can be used to explore proteins and their annotations trough a browser at http://3dbionotes.cnb.csic.es.

An API describing the different services to link and visualise external data is described at http://3dbionotes.cnb.csic.es/api.

3DBIONOTES web server source code and other JavaScript packages developed for biological feature visualisation are available at https://github.com/bioinsilico. 

c. Maintenance quality: Is there a maintenance SOP or plan, reflecting sustainability and scalability? Does it align with guidelines for sustainable software development? Please include a resource commitment statement (description text or URL).

3DBIONOTES project has been running for more than four years and it is a well-positioned project with stable funding from different sources. The project is funded by the Spanish Health System Institute Carlos III as part of the activities of the Spanish ELIXIR Node. Additionally, and since 3DBIONOTES has also a structural biology component, we have the stable funding of the Spanish Instruct-ERIC Centre.

In terms of resource commitment statement, 3DBIONOTES is the core of our contribution to the Spanish Node of ELIXIR and it is fully contained within the RoadMap presented and approved by the Spanish funding agencies in the context of the participation of Spain in ELIXIR. 

Although we do not have a formal SOP document, we basically follow the standard recommendations for sustainable software development
A new version of the application is released every year including new features, databases and tools. 

d. Support quality: Please list support mechanisms (e.g., point of contact, request ticketing, resource’s response time where a solution is identified, etc.), and methods to collect user feedback. If available, list tutorial documentations or tutorial materials and format, including linking on the ELIXIR’s Training Portal (TeSS) (or other training platforms) where applicable.

Contact mail 3dbionotes@cnb.csic.es

3DBIONOTES help page: http://3dbionotes.cnb.csic.es/ws/help
HOW TO tutorials (pdf) available online
• How to annotate a protein structure
• How to transfer annotations from homolog proteins

3DBIONOTES API description: http://3dbionotes.cnb.csic.es/ws/api

4. Legal framework, funding, and governance

a. Legal framework: What are the resource’s license/terms of use? Can the license facilitate Open Science? Please include the url for the license the resource uses.

LCENSE GPL3 https://www.gnu.org/licenses/gpl-3.0.en.html
3DBIONOTES platform is being developed as an open science project. The publications associated to this project have been published as open access and the source code is freely available in github under GPL3 license. 3DBIONOTES application is freely available for academic or industry use and no registration or log in is required.

b. Privacy/Ethics policy: If applicable, is there a publicly available privacy policy in which use and security around personal data are described (e.g. the EU General Data Protection Regulation (GDPR), ELIXIR Ethics Policy, other relevant ELIXIR Policies)? Please include the url of the privacy/ethics policy, if applicable.

Not applicable.

c. Funding & sustainability plan: List of funding sources supporting the resource, and sustainability plan.

We have stable funding from the Spanish Health System Institute Carlos III as part of the activities of the Spanish Elixir Node. Additionally, and since 3DBIONOTES has also a structural biology component, we have the stable funding of the Spanish Instruct-ERIC Centre.

d. Governance: Describe the Resource’s QA/QC plan that guarantees similar quality governance to that of ELIXIR. Please link SAB members, if applicable.

3DBIONOTES was evaluated positively by an external panel as part of the renewal of the ELIXIR-ES Service Delivery Plan (SDP). The ELIXIR-ES SDP will be introduced once the legal framework is renovated and approved by the ELIXIR Board. 

The committee was led by Dr. Jaume Bertranpetit (UPF, former director of ICREA), with the participation of Johanna McEntire (EBI, Co-lead of the ELIXIR Data Platform), Janet Kelso (Max Planck Institute for Evolutionary Anthropology, Vice-chair of ELIXIR SAB), Ioannis Xenarios (SIB, Vital-IT), and John Hancock (Earlham Institute, ELIXIR-UK Coordination node). The specific comments on 3DBIONOTES in autumn 2017 were:
“3DBIONOTES-WS is a resource that already demonstrates use in the community and which is well aligned with the aims of the tools and interoperability platform of ELIXIR. In fact, it is already integrated with EMDB-EBI (Electron Microscopy Data Bank), though this does not, itself, seem to be a part of ELIXIR. It would be good to work towards further integration with other data resources that form part of ELIXIR.”