# EDAM Browser

# 2021-05-21

## Attending
Hervé, Bryan, Hager, Matus

## Main topic

- https://www.outreachy.org/docs/community/#week-1-expectations

- Communication channels and meetings
- ✔ create private gitter channel @hager browser-outreachy202105
https://gitter.im/edamontology/browser-outreachy202105
- Office hours 9:30

## ELIXIR All Hands Meeting

- https://elixirallhands.eventscase.com/EN/meeting/Agenda

## BOSC abstracts submission deadline: 06/03

- submit abstract by next week @Hervé @Matus
- collect contribution information from github
- collect personal affiliation/contact info from contributors [Later]

- create personal info form: [Delayed for later; Actually doesn't belong here but let's keep it here for now, sorry for that]
- first name
- surname
- affiliation(s)
- public email
- private email or another preferred private communication channel
- location(s), country(ies) (can be different from affiliations)
- pronouns + consent to use
- ORCID
- link to the GoogleForm answer (to retrieve & edit data later)
- twitter
- GitHub
- BioPortal
- WebProtégé
- picture
- consent for code
- connection to name or BioPortal|WebProtégé username?
- consent for publications
- work on EDAM (for funding, costs, and engagement stats)
- volunteer (unpaid)
- as part of job description (funded)
- as part of other funded work
- "volunteer" as part of job with freedom

https://framaforms.org/content/creez-et-diffusez-vos-formulaires-facilement

## Task tracker

todo

## Action points

- ✔ Registration for ELIXIR All-Hands (@Hervé takes care)
- Form for contributors (@Matus will come up with the first version)
- ✔ Tracker for project management (@Hager to share with us. An option is using a public project in the edam-browser GitHub repo👍🏽)
- ✔ Drafting abstract for BOSC/ISMB (Who wants to start this? @Hervé? @Matus? @Hager? Together?)
- ✔ Give pointers to examples of posters and corresponding abstracts for EDAM, EDAM-poster, and other projects of interest to Hager (@Hervé and @Matus)
- EAH 2018 EDAM-browser [poster]( https://docs.google.com/presentation/d/1dgYIaxJMiJGj50KiZAf8JFq8yPZRLBzUIoo0gtJy5Xg/edit?usp=sharing)
- BCC 2020 EDAM poster, [abstract](https://bcc2020.sched.com/event/cvAS/p3-03-edam-the-ontology-of-bioinformatics-operations-topics-data-and-formats-update-2020) and [poster with an extended abstract](https://f1000research.com/posters/9-563)
- JOSS EDAM-browser [article](https://doi.org/10.21105/joss.00698)
- EDAM [article](https://doi.org/10.1093/bioinformatics/btt113)

# EDAM browser abstract for BOSC 2021

First name: Bryan [Last author✔]
Last name: Brancotte
Email: [e-mail]
Country/region: France
Organization: Hub de Bioinformatique et Biostatistique–Département Biologie Computationnelle, Institut Pasteur, Paris, France
Web page: https://research.pasteur.fr/fr/member/bryan-brancotte/

First name: Hager
Last name: Eldakroury
Email: [e-mail]
Country/region: Egypt
Organization: Ain Shams University, Outreachy intern (EDAM), Cairo
Web page:

First name: Sakshi
Last name: Dhamija
Email: [e-mail]
Country/region: India
Organization: ABV - Indian Institute of Information Technology and Management, Gwalior
Web page:

First name: Rashika
Last name: Rathi
Email: [e-mail]
Country/region: India
Organization: Indian Institute of Technology, Mandi
Web page:

First name: Drashti
Last name: Patoliya
Email: [e-mail]
Country/region: India
Organization: independent contributor, Surat
Web page:

First name: Sunday Cletus
Last name: Nkwuda
Email: [e-mail]
Country/region: Nigeria
Organization: freelancer, volunteer contributor, Outreachy intern (Debian), Kaduna
Web page:

First name: Guneet
Last name: Singh
Email: [e-mail]
Country/region: undisclosed
Organization: independent contributor
Web page:

First name: Pooja
Last name: Yadav
Email: [e-mail]
Country/region: India
Organization: independent contributor, Outreachy intern (LLVM), Goa
Web page:

First name: Kelly
Last name: D'oleo
Email: [e-mail]
Country/region: U.S.
Organization: independent contributor, New York City
Web page:

First name: Marlene
Last name: Cherop
Email: [e-mail]
Country/region: Kenya
Organization: independent contributor
Web page:

First name: Tawah Peggy
Last name: Che Nico
Email: [e-mail]
Country/region: Cameroon
Organization: University of Buea
Web page:

First name: Matúš
Last name: Kalaš (apapronominal)
Email: [e-mail]
Country/region: Norway
Organization: University of Bergen
Web page: https://orcid.org/0000-0002-1509-4981

First name: Hervé
Last name: Ménager
Email: [e-mail]
Country/region: France
Organization: Hub de Bioinformatique et Biostatistique–Département Biologie Computationnelle, Institut Pasteur, Paris, France
Web page: https://research.pasteur.fr/fr/member/herve-menager/

Title: **EDAM Browser: visualization of EDAM and bioinformatics resources**
Swankier title attempt: **EDAM Browser: visualization of EDAM, with a search functionality across registries**

Abstract (200 words max):
**EDAM is an ontology widely used to describe bioinformatics resources (tools, databases, workflows, training, etc.). However, the exploration of the ontology itself by users who might not be ontology experts remains sub-optimal, with most of the usual interfaces being either too complex, too slow, or too generic.
Here we present EDAM Browser, which lets users explore EDAM with an interface tailored to its structure and properties. The features of this ontology browser are focused on the needs of EDAM's end-users, who search and explore the ontology to find or annotate bioinformatics resources.
A unique feature of EDAM Browser is the visualization of all "positions" of a selected concept in the full ontology "tree" (DAG), with all paths to the root highlighted. One of EDAM Browser's main added values is the aggregated search across various registries (e.g. bio.tools, TeSS, BioSphere), and its speed.
The lightweight architecture makes it easy to download and run EDAM Browser on any server or personal computer, either as a local HTML file or on a web server. EDAM Browser has also been used for other ontologies, and making the reuse smoother and more usable is part of the ongoing work. Contributions are welcome!**

Submission Type.
**Poster Only**

Presenting Author.*
Please identify who will present this submission.

This research can also be considered for presentation in the following COSI (2nd Choice).
**No**

This research can also be considered for presentation in the following COSI (3rd Choice). Please select a 3rd COSI choice if applicable. Learn more about COSIs at: https://www.iscb.org/communities-of-special-interest
**leave empty**

Flipped Conference.* Would you be open to presenting in a "flipped conference" format where your talk video is made available to attendees some days in advance and the conference session will consist of a 2-minute summary presentation (preferably live), leaving more time for questions and discussion?
**Yes**

Previous Published Abstract. If your work has been previously published please identify year and Digital Object Identifier (DOI) - e.g. (2016)
10.1000/xyz123
**(2018) [10.21105/joss.00698](https://joss.theoj.org/papers/10.21105/joss.00698)**

Open Source License.* Work that is presented at BOSC must be licensed with a recognized Open Source or Open Content license. Please enter the name of that license in this field. For more info, see https://www.open-bio.org/events/bosc-2021/submit/
**MIT**

Link to your source code or content.* Please list the URL where your source code or other content can be found--e.g., GitHub or BitBucket repository URL.
**https://github.com/edamontology/edam-browser**

Registration fee reduction.* If we are able to provide registration fee assistance, do you want to be considered for a reduction in the conference registration fee? (Reviewers won't see your answer to this.)
**Yes**

Please briefly explain why you are requesting a reduction in the conference registration fee. (Answer only if you said "yes" to the registration fee assistance question above.)
Your response will not be seen by reviewers.
**We ask for a fee reduction for Hager Eldakroury (she/her, Egypt), who will be the main presenter of the poster, and is currently contributing to this project as an Outreachy intern. As an Outreachy intern she cannot get reimbursed by any of her affiliations. Additionally, we feel that providing fee reduction to participants from underrepresented groups in the community, or at the event, is very much aligned with the vision of BOSC and OBF.**

How will your participation increase diversity at BOSC/ISMB? BOSC aims to increase participation from groups otherwise underrepresented in the community or at the event, including but not limited to underrepresented demographic groups (country of residence and citizenship), ethnic background (historically underrepresented and other minority groups), career stages, gender identity and expression, and disabilities.
This question is optional, and your answer will not be seen by reviewers.
**We are actively working on increasing inclusion and diversity in the EDAM community (incl. EDAM Browser), by taking multiple actions, including our participation in the Outreachy program. By inviting our global contributors from underrepresented groups to BOSC, we are contributing to the diversity in BOSC and OBF.**

One more reason to add all relevant contributors, and mention improvements to inclusion and diversity thanks to "openness by design" and participation in Outreachy.

Video consent.* If your abstract is accepted for a talk, you will need to pre-record your talk (it's optional to include your face in the video). We like to make these videos available on the BOSC YouTube channel after the conference. Please indicate if you consent to having your talk video posted.
**Yes**

Consent for your slides and/or poster PDF to be shared.* We like to share BOSC slides and posters after the conference. Please indicate whether you consent to this.
**Yes**

Use of screenshots.* Do you agree to let us use screenshots of the conference (which may include your image) in reports, web pages, etc.?
**Yes**

Your time zone.* Please select the time zone you will be in during the conference in July. (Go to https://bit.ly/EDT-2020-07-20 and enter your city if you're not sure.)
**UTC+2**

Have you or will you present this work at other conferences? If so, please list. (We're still happy to consider your abstract for BOSC; we just want to know.)
**Yes, once at the ELIXIR All Hands in 2018.**

Comments for chairs. If there is anything else you would like the BOSC chairs to know, please enter it here. The reviewers will not see this field.
**leave blank**

The EDAM browser is available publicly and anonymously at https://edamontology.github.io/edam-browser/. It is downloadable from https://github.com/edamontology/edam-browser.

# Meeting 06/09

- Conference
- already registered to GCC, yay!
- ISMB/BOSC is TODO https://www.iscb.org/ismbeccb2021. @Hervé sees how
- @Hervé sees which deadlines and which poster(s) should be submitted to GCC