Entry version has disappeared from gene panel lists

[ielvers]

Hi,

When looking at our gene panels (https://scout.scilifelab.se/panels), I noticed that the entry version has disappeared from all entries in the panels (I've checked six different panels).

The panel Newborn screening, metabolic has also lost all inheritance terms.

Was this intended?

thanks,
Ingegerd

[dnil]

Hi @ielvers! Thank you for being on the lookout!

The entry version display was reworked #4957. You can see some of the discussion behind the change here: #4956. Bottom line, is as before only the new genes for the version are clearly marked "NEW" and the ones that were already in the panel are blank instead of showing the previous version. The full history can be seen as before by searching for a particular gene, or clicking through old versions, as before.

Loss of inheritance terms is not intended: I can see them fine for other panels, both newer and older. Just double checking, ofcourse you know they were there before for v17? And also v1? It's a little late, and my db connection is acting up, but I can reach the stage server. It has a v17 and a recent v18, both without any manual inheritance models annotated on the genes?

[dnil]

Not trying to lecture here, just thinking: do you think we could change how we communicate updates somehow? I can somewhat understand that users don't follow all discussions on the repo. But you do read through the change notes in each update email, right? 😊

[ielvers]

Re: entry version
I don't see the purpose of hiding the entry version. To me having all entry versions was much more useful than just seeing the genes from the latest update highlighted. All previous panel versions are not in the history section. Not a big deal though and good to know that it was intentional :)

Re: inheritance terms in NBS-M
You are correct, I can't say for sure that they were there before so I shouldn't say they were lost. This panel has only existed as v17. I don't check cases against this panel but I would assume someone would have mentioned if the manual inheritance was missing for all the genes. I asked a colleague who looks at cases with this panel and he couldn't say if the inheritance was there before or not. So maybe it was never there, and no one noticed.

Re: update emails
I always start reading the emails, but I rarely finish reading them. Most of the information doesn't mean anything to me, especially the technical stuff, so I kinda give up when reading them. I asked some of my closest colleagues and they don't read the emails because they don't understand the information. I want to stress that we appreciate Scout and you guys!! I checked a recent email now
[4.91.2]
Fixed

• Stranger TRGT parsing of . in [FORMAT.MC](http://format.mc/)
  - I'm sure this is important for something but info like this is why I stop reading lol
• Parse ClinVar low-penetrance info and display it alongside Pathogenic and likely pathogenic on SNVs pages - this sounds useful, awesome!
• Gene panel indexes to reflect the indexes used in production database - I have no idea what this means. I assume it's some internal numbering system you have for the different gene panels.
• Panel version check while editing the genes of a panel - I don't know what this means either.
• Display unknown filter tags as "danger" marked badges - means nothing to me. unknown filter tags? badges?
• Open WTS variantS SNVs and SVs in new tabs - this I can understand!

Again, Scout is a great tool and we very, very much appreciate all the work you all do. Sorry for asking about stuff that has been mentioned in an update email.

[northwestwitch]

Re: entry version I don't see the purpose of hiding the entry version. To me having all entry versions was much more useful than just seeing the genes from the latest update highlighted. All previous panel versions are not in the history section. Not a big deal though and good to know that it was intentional :)

Hi @ielvers, when you created a new panel version, entry version of all genes was always set to the previous panel version, automatically. This happened for genes introduced in the panel in the previous version or 10 panel versions before. We reasoned that for this reason that field was not informative and that's why we changed it. Sorry if it is confusing but the idea was to make it very clear when a gene is introduced in a panel for the very first time.

Re: inheritance terms in NBS-M You are correct, I can't say for sure that they were there before so I shouldn't say they were lost. This panel has only existed as v17. I don't check cases against this panel but I would assume someone would have mentioned if the manual inheritance was missing for all the genes. I asked a colleague who looks at cases with this panel and he couldn't say if the inheritance was there before or not. So maybe it was never there, and no one noticed.

There were several problems with inheritance terms and we made changes to hopefully fix the problem that panels could not be exported/imported and updated maintaining all available info from before. We have tested quite much before introducing these changes, but please let us know if you notice something that shouldn't be happening! 🙏🏻

Re: update emails I always start reading the emails, but I rarely finish reading them. Most of the information doesn't mean anything to me, especially the technical stuff, so I kinda give up when reading them. I asked some of my closest colleagues and they don't read the emails because they don't understand the information. I want to stress that we appreciate Scout and you guys!! I checked a recent email now [4.91.2] Fixed

• Stranger TRGT parsing of . in [FORMAT.MC](http://format.mc/)
  - I'm sure this is important for something but info like this is why I stop reading lol
• Parse ClinVar low-penetrance info and display it alongside Pathogenic and likely pathogenic on SNVs pages - this sounds useful, awesome!
• Gene panel indexes to reflect the indexes used in production database - I have no idea what this means. I assume it's some internal numbering system you have for the different gene panels.
• Panel version check while editing the genes of a panel - I don't know what this means either.
• Display unknown filter tags as "danger" marked badges - means nothing to me. unknown filter tags? badges?
• Open WTS variantS SNVs and SVs in new tabs - this I can understand!

Again, Scout is a great tool and we very, very much appreciate all the work you all do. Sorry for asking about stuff that has been mentioned in an update email.

For what's concerning the emails you are totally right, some things are not quite understandable by the software user. The most cryptic entries I would say are meant to be understood by scout administrators or developers in other institutions, so if you read something that makes no sense at all to you, please just ignore the info.

Regarding entries that update/change software behaviour, then it would be ideal that that information is understood by the users, so we'll try to be more clear with the descriptions. Sometimes it is hard because you have to describe a new feature of a fix to a bug with only one line. But If the message is not clear please reach out and ask, either to our emails or as you just did here! 👍🏻

But understood, we'll definitely make an effort to create clearer descriptions of the changes for the upcoming releases!