search

RNAcentral / rnacentral-webcode

RNAcentral website source code
https://rnacentral.org
Apache License 2.0
30 stars 9 forks source link

labels on browser "pull-down" menu #416

Open ValWood opened 5 years ago

ValWood commented 5 years ago

Hi,

I noticed for PomBase ter1 that:

rna

Some of the browser labelling seems odd.

  1. logic_name "pombase" seems redundant with "source" What does this mean?

  2. HGNC symbol SPNCRNA.215 just "symbol" would be more appropriate ...HGNC only applies to (some) metazoa

  3. The "symbol" is assigned for this entry, and the appropriate label "ter1" appears on the image, but not on the pull-down. This might just be a synching issue and will be solved when @kimrutherford makes the json

  4. Do you have a mapping of these labels to the json format ? For example is "name" here in the json https://github.com/RNAcentral/rnacentral-data-schema/blob/master/examples/flybase.json "name": "28S ribosomal RNA:CR45837", what we would use for product "description" in the pull down?

  5. Do you also have a list of definitions of the json format features?

ValWood commented 5 years ago
  1. Strand listed as "forward" but it is "reverse" ?
ValWood commented 5 years ago
  1. Do you need to display both "feature type" and "biotype"? ncRNA is_a gene ?
kimrutherford commented 5 years ago

Do you also have a list of definitions of the json format features?

The fields have descriptions here: https://github.com/RNAcentral/rnacentral-data-schema/blob/master/sections/ncrna.json

AntonPetrov commented 5 years ago

@ValWood Thank you for your feedback!

  1. logic_name "pombase" seems redundant with "source" What does this mean?

The fields come from the Ensembl REST API. The field logic_name refers to the name of analysis used to get the transcripts, which in this case is the same as the source. Perhaps we should review which fields are shown instead of showing everything that comes from the API.

  1. HGNC symbol SPNCRNA.215 just "symbol" would be more appropriate ...HGNC only applies to (some) metazoa

Good catch! @BurkovBA, could you please take a look? This is probably coming from the main Genoverse code.

  1. The "symbol" is assigned for this entry, and the appropriate label "ter1" appears on the image, but not on the pull-down. This might just be a synching issue and will be solved when @kimrutherford makes the json

It seems like the screenshot was taken after clicking not on ter1 but on a neighboring gene downstream. As far as I can tell, the correct label is shown for ter1:

screen shot 2018-08-28 at 7 52 30 am

  1. Do you have a mapping of these labels to the json format ? For example is "name" here in the json https://github.com/RNAcentral/rnacentral-data-schema/blob/master/examples/flybase.json "name": "28S ribosomal RNA:CR45837", what we would use for product "description" in the pull down?

  2. Do you also have a list of definitions of the json format features?

Are you thinking about submitting the data to RNAcentral in JSON format? If so, then @blakesweeney can prepare an example file and explain the meaning of all fields.

  1. Strand listed as "forward" but it is "reverse" ?

I checked all ter1 transcripts and they are consistently labelled as "reverse" (see the screenshot above). Please let me know if I am missing something.

  1. Do you need to display both "feature type" and "biotype"? ncRNA is_a gene ?

Thank you for pointing this out. We will review the fields that we show for Ensembl genes and transcripts in the genome browser. I agree that there is a lot of redundancy and the pop-up menu is not as useful as it could be.

Thanks again for raising this issue! We are eager to improve the way PomBase data are represented in RNAcentral and appreciate any suggestions for improvements. 🚀

ValWood commented 5 years ago

Strand listed as "forward" but it is "reverse" ?

Ignore, this is also the neighbouring feature!

BurkovBA commented 5 years ago

@ValWood Ok, so I assume that "forward"/"reverse" issue is a mis-click. Good, I'll switch attention to HGNC symbol. Thank you for the detailed feedback!

BurkovBA commented 5 years ago

@ValWood Renamed "HGNC symbol" to just "Symbol". As for the other improvements to the genoverse popup, we'll discuss redesign of its fields with the team later. Thank you.

AntonPetrov commented 5 years ago

I will keep this issue open until we revise the pop up menus for the Ensembl tracks. We will aim to do it for release 12. Thanks again for the feedback!

We will be happy to follow up any questions about JSON import by email or using GitHub issues in the rnacentral-data-schema repo.