Add tutorial for tool annotation with EDAM via bio.tools #4734
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| The annotation of tools can be done on [bio.tools](https://bio.tools/). bio.tools ({% cite ison2016tools %}) is a global portal for bioinformatics resources that helps researchers to find, understand, compare, and select resources suitable for their work. It relies on the EDAM ontology for standardazing the annotations. | ||
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| In Galaxy, tools can be annotated with EDAM terms, either by putting them directly in the wrapper or extracting them from their corresponding bio.tools entry by linking to it. The advantage of the second approach is that only one place (bio.tools entry) needs to store and keep updated EDAM terms. |
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| In Galaxy, tools can be annotated with EDAM terms, either by putting them directly in the wrapper or extracting them from their corresponding bio.tools entry by linking to it. The advantage of the second approach is that only one place (bio.tools entry) needs to store and keep updated EDAM terms. | |
| In Galaxy, tools can be annotated with EDAM terms, either by putting them directly in the wrapper or extracting them from their corresponding bio.tools entry by linking to it. The advantage of the second approach is that only one place (bio.tools entry) needs to store and keep updated EDAM terms. | |
| If the bio.tools entry for a tool is updated the information automatically propagates to the installed tool on a galaxy server, provided the tool is linked to its entry. |
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| # Choose a tool without bio.tool identifier | ||
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| To start, we need to select a tool without bio.tool identifier. |
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| To start, we need to select a tool without bio.tool identifier. | |
| To start, we need to select a tool without bio.tool identifier. If a tool is installed on a server the bio.tools entry will be shown on the bottom of the tool view. Another way to directly search for tools without bio.tools entry is the galaxy tool metadata extractor. | |
| <iframe id="edam" src="https://galaxyproject.github.io/galaxy_tool_metadata_extractor/" frameBorder="0" width="80%" height="600px"> </iframe> |
| time_estimation: 1H | ||
| key_points: | ||
| - Galaxy tools can get EDAM ontology terms from bio.tools | ||
| - bio.tools entry can be created and modified to provide the best EDAM annotations |
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Maybe we can add a point here?
- An up-to-date bio.tools entry provides readily accessible metadata that can help users to find and understand tools that are available on Galaxy
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Please consider using the "Suggestion Mode" feature of GitHub (see step 6).
By providing a suggestion using the proper suggestion mode:
- For authors, it is unambiguous what you are proposing
- It's also easier for them to simply accept the suggestion, PR authors prefer suggestions!
- You get credited in the Git commit helping us properly track attribution
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| Galaxy offers thousands of tools. A vast majority of these tools come with poor metadata. |
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Instead of "A vast majority" we could say:
Many of these tools either have incomplete metadata, or are not yet linked to sources of high quality metadata such as [bio.tools](https://bio.tools/).
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| layout: tutorial_hands_on | |||
| title: Annotation of a tool with EDAM ontology terms using bio.tools | |||
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Alternate title suggestion: Linking Galaxy tools to metadata in the bio.tools registry
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I feel that we cover more than just Linking in the tutorial. We cover also the aspect of creating bio.tools and improving the annotation on bio.tools
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What about: Adding and updating best practice metadata for Galaxy tools using the bio.tools registry?
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Some suggestions 😄 |
tutorial.md suggestions
| contributions: | ||
| authorship: | ||
| - bebatut | ||
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@supernord, @paulzierep add yourselves here
Co-authored-by: paulzierep <[email protected]>
| > 2. Click on **Add Condition** | ||
| > 3. Select *bio.tool id* in **Data** drop-down | ||
| > 4. Select *Empty* in **Condition** drop-down | ||
| > 5. Select a tool in the list |
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| > 5. Select a tool in the list | |
| > 5. Select a tool in the list, and proceed to the next section of the tutorial |
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We have an opportunity to also emphasise the addition of additional best practice metadata for bio.tools entries. |
Co-authored-by: Johan Gustafsson <[email protected]>
Co-authored-by: Johan Gustafsson <[email protected]>
On the principle it would be good but I am afraid people might be afraid it is too much work |
I would suggest making another tutorial if needed. |
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| > <hands-on-title>Find the Galaxy wrapper</hands-on-title> | ||
| > | ||
| > 1. Go to the tool on any Galaxy server |
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I think we should use the parsed source folder instead: galaxyproject/galaxy_codex#65
Which will be correct for all tools in our list.
For many tools I checked the location in the .shed file is wrong... that might confuse the helpers !
Co-authored-by: paulzierep <[email protected]>
Tutorial from the BioHackathon, needed for the galaxy_tool_metadata_extractor preprint galaxyproject/galaxy_codex#55 and the next microGalaxy hackathon galaxyproject/galaxy-hub#2404
@paulzierep, @supernord, @matuskalas, @nsoranzo: this is ready for review.
I will prepare the other one "Create an interactive Galaxy tools table for your community" next week