Automatic updating of the tools table and page metadata

[github-actions]

This PR is automatically generated based on changes in the tool_and_resource_list.yml file or updates in the page metadata. The updates are generated using the API of following registries/services:

• DSW
• FAIRsharing
• Bio.tools
• TeSS
• FAIR Cookbook

Please verify if these changes are valid.

[bianchini88]

Question: are these two distinct queries?

[bedroesb]

I do not understand this question 🤔 The toolname gets filled in fully or without acronym in: https://github.com/elixir-europe/rdmkit/blob/master/var/tools_validator.py#L67

[bianchini88]

This query does not bring up anything https://tess.elixir-europe.org/search?q=ENA+Reads+Assembly+Submission+Workflow, so I am wondering why this is added.

[bianchini88]

But if I take only the first part, I get https://tess.elixir-europe.org/search?q=ENA+Reads+ which works.

[bianchini88]

If you paste the tool.name in the string you highlight, you get this, which does not quite look like the query we want. Could it be that the "&" symbol in the name is messing things up?

[bedroesb]

I assume the acronym splitting regex is doing funny things, needs some local debugging I am afraid

[bianchini88]

@bedroesb, we have closed #1847, which is good, but the original problems still remain. What do you think we should do? OMOP disappearing is not good, and the "ENA Reads & Assembly Submission Workflow" is still unclear to me.

[bedroesb]

@bianchini88 I am adapting the ETT to also have the strict search when linking to TeSS. I cannot make an exception to do a lookup for only OMOP using the acronym, we choose not to do acronym only lookups with TeSS because it resulted in to many false positives. I suggest to rename to one with a results, or excepting that we lose the link in this case. There is no ideal solution I am afraid and I would choose the latter. The "ENA Reads & Assembly Submission Workflow" is still unclear and I will look into it now.

[bianchini88]

I cannot make an exception to do a lookup for only OMOP using the acronym, we choose not to do acronym only lookups with TeSS because it resulted in to many false positives.

Fully agree. I am a curator on TeSS (although it is an unclear role), so I added the FAIRsharing annotation to an entry. The FAIRsharing record happens to have the same name we have in our table (I might have made them match myself in the past, can't quite remember). Anyway, this results in the exact query getting a hit:

https://tess.elixir-europe.org/search?q=%22Observational+Medical+Outcomes+Partnership+Common+Data+Model%22

So this should solve the first problem, shouldn't it? @bedroesb

[bedroesb]

@bianchini88 corect!

[bianchini88]

@bedroesb Ok, so that one will correctly disappear, and the correct query will appear next Monday, so that is solved.

[bianchini88]

I removed the "&" symbol. Maybe this helps (or maybe not), but the actual citation from WorkflowHub is

Droesbeke, B. (2025). ENA Reads and Assembly Submission Workflow. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.2008.1

[bedroesb]

@bianchini88 I've reran the action on this branch. Looks good now?

[bianchini88]

This does not look right https://tess.elixir-europe.org/search?q=%22PAA%22. We should spell out the name.

[bianchini88]

This is correct. We will lose the entry if we were to spell out this into "Structure integration with function, taxonomy and sequence". I would suggest leaving as is, as this acronym is probably not too ambiguous.

[bianchini88]

Why are we getting the acronym here? It does not do any harm, but we typically do not get one.

[bedroesb]

Because (DSW) only got added recently and because it first tries with the full name, and if it picks up hits, it chooses that one.

[bianchini88]

Ok, so there are no materials on TeSS for this, but there are plenty of old events https://tess.elixir-europe.org/events?include_expired=true&q=Inkscape. So this is an annotation that will move back and forth depending on whether a new workshop is scheduled or not. We should probably decide whether old events are relevant information or not (they certainly are useful as track records of the resource, but they are not immediately useful to the end-user, especially since the materials are not registered on TeSS; but they could be registered somewhere else).

[bedroesb]

This is not to up for decide but a TeSS question no?

[bianchini88]

Well... it is up to us to decide whether we are happy with a "floating annotation" or not, and whether the specific queries for events (which is the only way of showing the ones that happened in the past) are relevant or not.

[bedroesb]

But the weekly updates should prevent the accumulation of floating annotations, no? And specific queries for events should not replace the general query in my opinion. And having two links to TeSS per tool (potentially), sounds a bit excessive. I would be open to the opposite, only linking to Training materials and no events.

[bianchini88]

Let me explain. If there is an event scheduled in the future, then the query has one hit and the annotation is added. After the event has ended, the same query no longer has a hit, and the annotation thus disappears.

And specific queries for events should not replace the general query in my opinion.

I agree, obviously.

And having two links to TeSS per tool (potentially), sounds a bit excessive.

On one side I agree it could be excessive, on another one could argue that these are distinct subregistries of TeSS. I do not have an opinion honestly, I am mostly pointing out possibilities.

I would be open to the opposite, only linking to Training materials and no events.

This would lead to cleaner results (i.e. no floating unless the materials is explicitely marked as outdated by the creator or curator, which is just fine). To be fair, considering we are writing explicitly "[topic] Training materials in TeSS" at the bottom of our pages, this would be the correct thing to do.

[bedroesb]

I agree with you train of taught, but this PR is not about the TeSS links at the end of the page using the structure you specify, but for the registry tags in the tools table. A change to training materials only should be aligned with a ETT change since the pattern is hardcoded.

[bianchini88]

but this PR is not about the TeSS links at the end of the page

Very true!

A change to training materials only should be aligned with a ETT change since the pattern is hardcoded.

One could argue that ETT should offer more possibilities/alternatives, and it comes down to the users to decide which ones are relevant and which ones are overkill.

[bedroesb]

Action seemed to have force pushed on top of our commits. Lets merge and see what the GitHub Actions will bring next time