Comment field rules

[ValWood]

Figures tend to be referenced in journals in 2 ways
(Figure 6B)
or
(Fig. 6B)
AND we usually now copy/poast directly from the text

However when we have added "figure refs" manually we have used a lot of random ways.
I wonder if these can be "fixed up"

i.e
1 change all
fig to Fig
figure to Figure
Fig to Fig.
Add a space to any Fig3B -> Fig 3b
Figure 1 C -Figure 1C
Put parentheses around all Figure/Fig. with their alpha numerics.

Ones like these
PMID:11432827 FYPO:0001491 2C
PMID:11432827 FYPO:0002060 2C
PMID:11432827 FYPO:0000324 3f
PMID:11432827 FYPO:0004317 1A
PMID:11432827 FYPO:0000131 1A

need (Fig/Figure inserted)

If you can do the ones that you can automatically, I can do the remainder manually (or it doesn't matter if a few remain)

[ValWood]

Other things to do with this file

• The word "background" occurrs 179 times. Presumably these can move to background...

• Quite a lot of the comments are places where I was waiting for new GO terms etc and I didn't go back and add them
  e.g
  PMID:18061564 GO:0051256 FORMATION
  PMID:18061564 PBO:0099331 minus end
  PMID:18061564 PBO:0099333 activation

• 45 "http, mainly github tickets)

[ValWood]

• 40 homozygous diploid predate our ability to create diploid genotypes, probably other mentioning diploid

[ValWood]

We also need to similarly semi-standardize Table numbers and Supplemental data

I think in the first instance, we should only export lines which have a Figure or Table reference included. This will exclude most of the irrelevant information.
We can also exclude anything (comment: *)

One problem might be that this file only has comments for some of the curated data, not for every annotation.
We can discuss any problems this might cause with end users.
I wonder if we even have any sessions where every annotation is supported by a reference to a figure or table?

[PCarme]

Other things to do with this file

• The word "background" occurrs 179 times. Presumably these can move to background...

I can start with these ones, should be pretty straightforward.

[ValWood]

I can start with these ones, should be pretty straightforward.

you are a star. I will try to straighten up most of the rest. It doesn't need to be perfect, but it is also a good opportunity to improve the curation by converting notes into standard annotations...

[PCarme]

Other things to do with this file

• The word "background" occurrs 179 times. Presumably these can move to background...

I looked at these, actually most of them look like quotes from the articles that contain the word "background".
I still fixed the ones that were clearly referencing the strains background, as well as a few other comments with informations that could move to another category that I saw in the sessions.

[kimrutherford]

1 change all
fig to Fig
figure to Figure
Fig to Fig.

Would it be better to standardise all these as "Figure "?

[kimrutherford]

Put parentheses around all Figure/Fig. with their alpha numerics.

So change "Fig 2" to "(Fig 2)"?

What format should be used for comments like this?:

Fig. 4, B and C)I

[ValWood]

Probably.
Some journals use Fig. and some use Figure and I wondered if maybe the existing was related to this (I now copy and paste it so it should always be one of these 2). We could standardis but new ones will often be (Fig. )

[ValWood]

So change "Fig 2" to "(Fig 2)"?

Yes, Fig. and Supp dat references should always be in parentheses

[ValWood]

Fig. 4, B and C)I

Is probably a typo of
(Fig. 4, B and C) so I would leave it out. I can review these "odd bods" when I scroll through the text later.

[ValWood]

Fig. 4, B and C)I
I just checked and figure 4 doesn't have a panel I, deleted