EDAM ontology, tool information, _etc._

## BioHackEU20 project nr. 10 # EDAM ontology, tool information, _etc._ **Slack channel:** 10_edam **This HackMD doc:** Please notify on Slack or Remo whiteboard if you have problems editting this doc. * **Please add any notes or questions to the end of this doc.** * And please add sub-points to the already present points. ## Planned meetings **Next:** * Fri 10:00-12:30 UTC (11:00-13:30 CET) Concluding presentations of all projects, in Remo. **Please add any planned meetings within euBH20 here**, that are relevant to the EDAM project: * * * And please watch this space, or the Slack channel, or the Remo whiteboard for announcements. ## Project outline **Aims:** * Help everyone who needs help with using/adopting EDAM **(various in progress)** * Extend EDAM with open science and FAIR data management concepts **(collaboration started)** * Update BLAST formats **(in progress)** * Optional: Work on tool information profiles and EDAM tools * For more see [Notes..](#Notes-questions-comments-and-answers) below **(various in progress)** **Outcomes:** * New collaborations **(2 started, 1 resumed)** * New PRs in EDAM **(1 so far, more soon)** * Optional: New website **(in progress)** **Expertise:** * Experts in open science * Optional: Python or JS hackers ## How to edit in HackMD If you see this page in **view mode**, what you probably do after opening it, click on *Edit* on the top. Later you can always do either of the following to enable editing: 1. **Edit mode**: Ctrl+Alt+E, or click the button with a pencil on the top left to switch to edit mode 2. **Both mode**: Ctrl+Alt+B, or click the button with a square with a vertical line in the middle (among the 3 buttons on the top left). Nice with a big-enough screen. ## Achievements * Navigation in Galaxy tools panel using EDAM (awesome work from [@hexylena](https://github.com/hexylena) right before BioHackEU20) * Publication of _biotoolsSchema_ data model for tool information ([@hmenager](https://github.com/hmenager), [@joncison](https://github.com/joncison) _et al._) * Major step towards longer-term sustainability of EDAM ([@matuskalas](https://github.com/matuskalas), [@sveinugu](https://github.com/sveinugu), [@korbinib](https://github.com/korbinib)) * New collaboration started on open science and FAIR data management concepts in EDAM (see below) * Kicked off work on refining EDAM to support genomic track characteristics for TrackFind/FAIRtracks ([@sveinugu](https://github.com/sveinugu), [@matuskalas](https://github.com/matuskalas), [@hmenager](https://github.com/hmenager)) * Sync with Debian Med on providing updates of package information ([@smoe](https://github.com/smoe), [@hmenager](https://github.com/hmenager), [@matuskalas](https://github.com/matuskalas)) ## Notes, questions, comments, and answers Please **add notes or ask new questions at the bottom** of this document. You can ask anonymously, or write your name. * writing e.g. `[name=Lisa]` will show up as [name=Lisa] ------------- * A sample question: How to write a question using **markdown** in HackMD? * You can just add a new line or a couple, and you can add a bullet point (`*`), use **bold** or *italics*, [links](https://mitt.uib.no), etc. * You can nest and indent bullet points under each other like this (using tab or at least 2 spaces) * **Topic: Open science and data management concepts in EDAM** * -> **_N.B._:** The communication channel for this work is within the **ELIXIR-CONVERGE Slack: _#edam-for-datamanagement_** <- * Objective: Improve the coverage & modelling of the main concepts in open science and data management * What has been in EDAM is a bit too bioinformatics-specific, and generic concepts (like Open science or Open data) have previously been omitted * A neat coverage of the main concepts with relevant relations, without going deep into the nitty-gritty details of data management, will be useful _e.g._ in annotation of training materials/events or tools. * Collaboration with folks from Project nr. 29 Learning Paths (29_learningpath) and Project nr. 2 DSW (2_datastwizard on Slack) in addition to nr. 10 EDAM (10_edam): Celia, Patricia, Rob, Marek, Hervé, Matúš * **Decided next steps:** * Form a group that will further work on this (incl. stakeholders from 4 ELIXIR Platforms & ELIXIR-CONVERGE, **and interested experts in open science and data management**, from anywhere) * Use cases are annotation of: * training materials|events * skills * tools * The scope will more precisely crystalise as we discuss it thoroughly in the future group * incl. eventual links to specialised ontologies beyond EDAM, or even ways to merge various related ontologies into some semantic data models (for more complex use cases than ones listed above) * The [request from Victoria and Pascal](https://github.com/edamontology/edamontology/issues/581) to create the FAIR related terms in EDAM will be delayed until the group has achieved a set of actions/recommendations * * -> **_N.B._:** The communication channel for this work is within the **ELIXIR-CONVERGE Slack: _#edam-for-datamanagement_** <- * * **Topic: Update of BLAST formats** * Afterwards update also BLAST tools in _bio.tools_ * Don't forget MagicBLAST * A lot of BLAST documentation is now moved to GitHub * Ask the "BLAST-locals" for help * * * **Topic: Tools navigation in Galaxy using EDAM** * First version now ready by [@hexylena](https://github.com/hexylena), hooray!! * We'll have to iteratively further work on the underlying info: a) Annotations of Galaxy tools and improvements of the annotations b) Improvements in EDAM itself so that the UX is great * * * **Topic: Genomic tracks / sequence annotation characteristics in EDAM** * The following are the current needs from the TrackFind/FAIRtracks toolkit & schema * EDAM Formats (some minor updates|additions might be needed) * Kinds of genomic tracks (should somehow be refined in EDAM Data) 1. Track data files are in one way or another a condensed representation of the raw data. EDAM already contains file formats, as well as generic data types, while other ontologies are focused more on terms describing biological entities, experimental techniques or genomic features. But there is a level in-between those, which would be very useful to have some vocaulary for. For instance the term "Peaks" is not really defined in any ontology I [@sveinugu] have seen. Examples here: https://github.com/fairtracks/fairtracks_standard/blob/master/docs/fairtracks_track.md#type_of_condensed_data-constraints 2. This is a complete geometrical delineation of possible track types, published in this paper: https://www.doi.org/10.1186/1471-2105-12-494. This relates both to how tracks are visualized and also how they are analyzed (e.g. do the elemenths have lengths? Associated values? Links to other elements?). Full list here: https://github.com/fairtracks/fairtracks_standard/blob/master/docs/fairtracks_track.md#geometric_track_type-constraints * Recent example of (independent) paper that makes use of these concepts: https://doi.org/10.1111/cgf.13727 * There is a mapping between 1. and 2., but it is not neccessarily 1-to-1. * Some "condensed data constraints" are specific to 1 or more of the "geometric constraints", aren't they? * Some data formats are specific to 1 or more of the "geometric constraints" * Any pointers to ontologies containing concepts that describe: * Data use policy? * Data/metadata licensing? * These might be questions to the data management experts (*e.g.* 2_datastwizard or [@korbinib](https://github.com/korbinib) or .. . Perhaps Rob?) * **Topic: Package annotation in Debian** * Bio.tools & the Tools Platform Ecosystem publish data about Debian packages and use annotation from Debian * We also want to be able to issue updates to packages in Debian if there are more up-to-date annotations available in bio.tools|tp_ecosystem * Further details discussed by [@smoe](https://github.com/smoe), [@hmenager](https://github.com/hmenager), [@matuskalas](https://github.com/matuskalas) in a dedicated thread (*[Metadata exchange with the Tools Platform Ecosystem](https://lists.debian.org/debian-med/2020/11/msg00148.html)*) on the Debian Med mailing list ([join](https://lists.debian.org/debian-med/)) * * * [name=Matus] Another sample question: What to ask? * ... * .. * blahblah * **Please add topics below here**, or add comments to the topics above... * * * * * * * * *