BISE Bioimage Informatics Search Engine

1. Resource facilitation to scientific research

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

BIII Bio Image informatics Index (www.biii.eu) is a knowledge database of software tools, test image databases and training materials for bio image analysis.

Software tools are organized as full protocol of analysis (workflow), specific brick (component) to construct a workflow, or software platform or library (collection). They are classified using Edam Bio Imaging, an extension from EDAM, which is iteratively defined using this website. All entries are exposed following FAIR principles and accessible for other usage with (ODC-By) v1.0 license.

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.

The scope is to provide an entry point for the community of bio image analyst and biologist using imaging in their research. In order to help the community to find possible components or existing workflows among the plethora of available software, we provide :

1) a common vocabulary and definitions related to this field

2) a unique entry point to search and compare software available,

Some of these software tools also have the potential to be used for a different purpose of life scientists and developers contribute to cataloguing the applicability of existing tools to image processing or biological problem, and imaging modalities by sharing their own knowledge and experience by the newly established community of bio image analysts. By associating biological terms (such as microtubules, vessel) to image processing task (such as filament tracing), we aim to help users find tools without the knowledge of image processing terms. Similar initiative exists either for a broader range of applications bio.tools, eitheir for more restrained application topics www.plant-image-analysis.org or COMULIS a user community of correlated multimodal imaging, getting directly their data from biii.eu data exposition : (prototype) https://www.comulis.eu/correlation-software-porto2019 . Compared to bio.tools : we are aligning with bioschemas in order to allow a direct import of the software to bio.tools.

Documentation is available on biii.eu/about, as well as on the wiki https://github.com/NeuBIAS/bise/wiki

An entry exist on Bio.tools : https://bio.tools/BISE

c. Resource url

https://biii.eu

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)

This resource has been created in the context of a European network COST NEUBIAS CA 15124 . We have about 243 people contributing by curating tools, called taggers, mainly from Europe, but also from North and South America , and Asia. We organize twice a year « taggathons » . Each taggathon has been associated with a boost in the number of curated tools, but taggers are also now constantly adding new tools or editing former ones. The taggathon are also the place where web development is done, as well as the work on the Edam Bio Imaging ontology (in collaboration with ELIXIR) , and core ontology (in collaboration with ELIXIR-FR). Taggathon has been funded by EUBI, France BioImaging, and several institutes has paid for the travel fees of contributors. We are also part from the Service Delivery Plan of ELIXIR-FR.

2. Community

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

For now, we are used by https://idr.openmicroscopy.org/about/itr.html , cost action COMULIS https://www.comulis.eu/correlation-software-porto2019 . Forum.sc (a collaborative framework between most of the platform of bio image analysis) refer to biii.eu entries regularly. Other unpublished tools have started to use biii.eu as well, for example BIAFLOWS, a benchmarking platform of image analysis tools https://www.biorxiv.org/content/10.1101/707489v1.

API calls can be done, some demonstration of advanced query using our API are provided on a mybinder server : https://mybinder.org/v2/gh/NeuBIAS/bise-core-ontology.git/master?filepa… .

All data can be exposed in JSON (example http://biii.eu/soft?_format=json).

We expose our data following two ontologies http://bioportal.bioontoly.org/ontologies/EDAM-BIOIMAGING and http://visualdataweb.de/webvowl/#iri=https://raw.githubusercontent.com/… , the latest beeing in the process of beeing aligned with Bioschemas.

The home page has for now 16497 views, all 1327 software entries total 48883 views, with an average of 37 view by software, 8.7 % of software having more than 100 views each.

In addition the work on EDAM bio imaging is creating links between the bio image informatic community , and the regular bio informatic one (usually more focused on -all omics but image- data), : some people from our community (Imaging community) has discovered the existence of elixir through biii.eu .

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

The ITR from EUBI et GBI is only referencing biii.eu and got some entry manually from it, while an automatic export could be done using our API. We also believe that a minimum effort we could feed automatically our entries to bio.tools .

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).

Documentation for end users is provided http://biii.eu/about and documention for taggers is here : http://biii.eu/howtocurate. We have a wiki and a github for the developmebt part of the tool : https://github.com/NeuBIAS/bise/wiki

A publication is under preparation and will be submitted to Nature Methods , after discussion we already had with one of the editors. The resource has been presented at several conference (NEUBIAS, COMULIS, ASCB,..) over the past 5 years and we plan to go on with the organization of the taggathon. We take attention to have a turn over in the list of invited taggers, in order to have new people and to raise the awareness of the tool. In addition, Biii.eu is now also part of the training course module of image analysis courses (at least 4 courses a year) that bio image analyst part of our network organize, following the concept of "Learn to fish", as well as a newly established EMBO course on advanced bio image analysis.

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.

We rely on Edam bio imaging and Edam bio imaging relies on the resource : indeed, we provide a easiest mechanism for the suggestion of new terms and synonyms for edam bio imaging than using webprotege, which may sounds less easy to access for most of the users in our scope. Our mechanism is used for the update of the ontology. In addition, the other resources that we have mentioned (such as COMULIS , ITR EUBI or BIAFLOWS) rely on us.

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 resource has been responsive 100% of the time since its first release in 2014. For this , we rely on the following scheme of development : a docker for local dev on the dev own computers, which are requested as pull on a git hub when ready. This pull is then deployed to a test dev environment, and released when validated by another developer : http://test.biii.eu/. The edam ontology updates are released once a year, the software release cycle frequency is at least twice a year. Data are edited daily by taggers (either new entries, either completing existing entries).

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.

The basic use of the software relies on a web interface, constructed upon DRUPAL 8.0. The application programmable interface can be extended infinitely and allow the full access to the database. Example of JSON access includes http://biii.eu/soft?_format=json.

RSS export is also available http://biii.eu/rss-export or biii.eu/rss.xml.

Tools associated with a particular taxonomy , or a specific Search are also exposed (they are used for example in comulis)

http://biii.eu/taxonomy/term/4055/json?_format=json
http://biii.eu/search?search_api_fulltext=registration
http://biii.eu/wfsteps?_format=json

A Juniper notebook demonstrate the use of the data

https://mybinder.org/v2/gh/NeuBIAS/bise-core-ontology.git/master?filepa… for Advanced queries and information mining such as creating hot map of topics against operations.

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).

The outline of the development is here: https://github.com/NeuBIAS/bise/wiki/BISE-development. In a few words, a developer can use any operating system to contribute to the development of the web tool itself. Dependencies are managed through landro and docker, and directly linked to our GitHub. A clear workflow of development is provided.

Database content is saved daily, and 3 back ups are constantly kept: the day before, the one week month version and the one month version.

From the taggers 'curators' point of view all the curation is done from the web interface, with mechanisms of "batch tagging" allowed for expert users (confirmed taggers).

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.

We use both http://biii.eu/forum and a git ticket system https://github.com/NeuBIAS/bise/issues which is the one mostly in use.

Tutorial for curation are available here:

• http://biii.eu/howtocurate

Tutorial for more Advanced users is here:

• https://github.com/NeuBIAS/bise/wiki/BISE-overview
• https://github.com/NeuBIAS/bise/wiki/BISE-project-and-community
• https://github.com/NeuBIAS/bise/wiki/BISE-and-Edam-Bio-Imaging

Tutorial to contribute to the development is here:

• https://github.com/NeuBIAS/bise/wiki/BISE-development, including a GitHub help:
• https://github.com/NeuBIAS/bise/wiki/BISE-Github-Workflow

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.

This database BISE is made available under the Open Data Commons Attribution License (ODC-By) v1.0 . https://opendatacommons.org/licenses/by/1.0/

In summary, users are free to share , reuse and adapt BISE, as long as you credit BISE, NEUBIAS and its contributors. All data can then be reused.

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.

Because the look and feel of biii.eu is under dev test.biii.eu, we did not updated the registration page yet but it will be done at the next release first week of March:

https://github.com/NeuBIAS/bise/issues/87

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

We were funding under COST ACtion NEUBIAS until May 2020. COST Action COMULIS has now committed also to support the next taggathons (until May 2023). We are also now applying to an INFRA-IA Starting Community, and plan to Apply to the next Chan Zuckerberg call . Note that the main contributors have permanent positions.

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

Our ressource is completely bottom up: we discuss with the core maintainers the proposals from the communities .

SAB:

• Perrine Paul-Gilloteaux
• Kota Miura
• Chong Zhang
• Alban Gaignard
• Matus Kalas
• Leandro Scholz
• Florian Levet
• Julien Colombelli