Generate a ranked list of modifications that need colors; provide PRO examples

[nataled]

Create a list of the MOD slims, ranked by usage within PRO and Reactome AT SPECIFIC SITES ONLY, that will need highlight colors. Should also include those that won't get a background color but will need a border color. For each of these, we want at least one PRO example--even better if the example requires multiple colors.

[nataled]

Background color only:

6232 MOD:00677 hydroxylated residue
4533 MOD:00696 phosphorylated residue
3956 MOD:00764 glycoconjugated residue
1109 MOD:90002 peptide-linked
 817 MOD:90004 sequence variant
 437 MOD:01152 carboxylated residue
 270 MOD:02078 acetylated residue
 268 MOD:90001 lipoacylated
 240 MOD:90003 other
 226 MOD:00427 methylated residue
 205 MOD:00033 crosslinked residues
 189 MOD:00703 isoprenylated residue
 135 MOD:00674 amidated residue
  48 MOD:00701 nucleotide or nucleic acid modified residue
  43 MOD:00675 oxidized residue
  20 MOD:00649 acylated residue
  -- --------- conserved site
  -- --------- conserved substitution
  -- --------- mouse-over column highlight

Border color only:

 152 PR:000026291 unmodified
 

Note 1: The above numbers are per-proteoform. Thus, if a proteoform contains 3 phosphorylated residues, it counts as 1.

Note 2: The sequence variant numbers are underestimated, as there isn't a good way to get that info for Reactome without doing more work than is warranted.

[nataled]

Here is a link that shows the color selection: https://proteininformationresource.org/staff/nataled/modification_colors.html

I didn't really worry about precisely which modifications get which colors; for now the concern is the set to use and which text color should go with each color. To this end, each color is shown twice, once with black text and one with white text (though I removed the ones that definitely don't work).

A few specific questions for all:

1. For the cases where there are both black text and white text choices, do you agree with the selection made in the column labeled 'Text' for that color?

2. Which color should be used as the column-highlight color (orange in the current implementation, red in my chart). I'm not very concerned about the accessibility (% population that can see the color) because the highlighting is moveable and thus can be seen on that basis. The more important aspect of the column highlight is that the color should work with both text options (because the text color itself doesn't change when highlighting the column, even though the background color changes to the highlight color).

3. 'Conserved substitution' doesn't seem to currently work, regardless of how it's interpreted (see note in link). I don't really think it's needed anyway, as I think we can just rely on the user to know when the substitution is conserved (say, S to L at aligned position in both human and mouse) or conservative (say, S to T at aligned position). Do you agree that it is not needed?

Please answer these questions before we go on to more detailed issues.

1. agree or disagree
2. color for highlight (can be multiple; please rank if so)
3. agree or disagree

@Julie-Cowart @karenross @chumingc @hongzhanhuang @jz26

[karenross]

1. I think orange should have black text and possibly also magenta. In general, I think the black text is easier on the eyes and should be used whenever it is a borderline case. 2. I agree red is good for highlight color. I also like green. 3. "Conserved substitution" is meant to refer to cases where a PTM residue is substituted for another residue that can undergo the same PTM. Mostly, we use it for S --> T or T --> S substitutions at phosphorylation sites. (I can't recall if we also mark S/T --> Y and Y --> S/T as conserved). I think this is an important point to highlight if we can; however, conserved substitution is a confusing name for it. Also, do we need a color for multiple--for example, a sequence variant that undergoes PTM?

…

On Mon, Sep 27, 2021 at 6:38 PM Darren A. Natale ***@***.***> wrote: Here is a link that shows the color selection: https://proteininformationresource.org/staff/nataled/modification_colors.html I didn't really worry about precisely which modifications get which colors; for now the concern is the set to use and which text color should go with each color. To this end, each color is shown twice, once with black text and one with white text (though I removed the ones that definitely don't work). A few specific questions for all: 1. For the cases where there are both black text and white text choices, do you agree with the selection made in the column labeled 'Text' for that color? 2. Which color should be used as the column-highlight color (orange in the current implementation, red in my chart). I'm not very concerned about the accessibility (% population that can see the color) because the highlighting is moveable and thus can be seen on that basis. The more important aspect of the column highlight is that the color should work with both text options (because the text color itself doesn't change when highlighting the column, even though the background color changes to the highlight color). 3. 'Conserved substitution' doesn't seem to currently work, regardless of how it's interpreted (see note in link). I don't really think it's needed anyway, as I think we can just rely on the user to know when the substitution is conserved (say, S to L at aligned position in both human and mouse) or conservative (say, S to T at aligned position). Do you agree that it is not needed? Please answer these questions before we go on to more detailed issues. 1. agree or disagree 2. color for highlight (can be multiple; please rank if so) 3. agree or disagree @Julie-Cowart <https://github.com/Julie-Cowart> @karenross <https://github.com/karenross> @chumingc <https://github.com/chumingc> @hongzhanhuang <https://github.com/hongzhanhuang> @jz26 <https://github.com/jz26> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#259 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMFDAAD7B5BJQZYLVOJ3P63UEDW7NANCNFSM5EWO2NDQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[nataled]

To discuss at the next meeting, but a few quick comments:'

1. I agree that black text is easier on the eyes, but here we're more concerned with contrast.

2. Eligible colors, IMO, are those that allow seeing both black and white text, AND are in the 95 or 99 percent range (saving the higher percent colors for specific highlights). That gives pink, magenta, cyan, green, and red.

3. The need for a color for multiple, to me, comes down to what we want to draw attention to. My opinion is that the PTM is the more important aspect, and that highlighting in two different colors for the same PTM is likely to result in the user thinking there are two different PTMs.

Regarding the third point, what are considered conserved substitutions? Let's say S35 in a human protein is phosphorylated, and there is a sequence variant in which S35 --> T35, and it too is phosphorylated. I presume this definitely fits the case. But what if the natural protein in mouse is T35, and it's phosphorylated. Does that count as conserved substitution?