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JervenBolleman / FALDO-paper

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Claiming to handle all biological uses cases #11

Closed peterjc closed 10 years ago

peterjc commented 10 years ago

We have a strong evidence of its power in that FALDO can handle all of the annotations in INSDC/DDBJ and UniProt, but biological systems have a habit of throwing up more strange cases. However, I feel that the current wording in the abstract and conclusion is too strong, "expressive enough to describe all known biological use cases accurately" and "power to describe all biological feature positions". As a reviewer I would ask for this language to be toned down.

peterjc commented 10 years ago

Also raised by @ktym by email, "Is it capable to represent repeats, indels, alignments, genome rearrangement etc.?"

I was also trying to think of problem cases - my first observation is that FALDO only considers positions as integer co-ordinates along a linear (possibly) circular reference sequence. This is a problem for branched sequences, such as modified proteins, or other polymers. Sticking to proteins and nucleotides, we are focused on the primary structure (co-ordinates along the sequence), without direct consideration of secondary or tertiary structure (e.g. alpha helices, tRNA hairpins, dimers). Toshiaki's examples may also be problematic depending how they are approached.

peterjc commented 10 years ago

Closing this issue as fixed in https://github.com/JervenBolleman/FALDO-paper/commit/50c04abf5626dc2b98fc3aa0e3812342eda79121

peterjc commented 10 years ago

Actually the conclusions still say all which feels is a bit too strong,

The diverse software and high-profile databases already using FALDO show that it
has enough power to describe *all* biological feature locations.

How about?:

The diverse software and high-profile databases already using FALDO show that it
has enough power to describe existing biological feature locations.
JervenBolleman commented 10 years ago

Look very good to me. Do you have patch ready? or should I commit it?

On Mon, Jan 27, 2014 at 6:24 PM, Peter Cock notifications@github.comwrote:

Actually the conclusions still say all which feels is a bit too strong,

The diverse software and high-profile databases already using FALDO show that it has enough power to describe all biological feature locations.

How about?:

The diverse software and high-profile databases already using FALDO show that it has enough power to describe existing biological feature locations.

— Reply to this email directly or view it on GitHubhttps://github.com/JervenBolleman/FALDO-paper/issues/11#issuecomment-33398405 .

Jerven Bolleman me@jerven.eu

peterjc commented 10 years ago

If you're still in front of a computer, go ahead. Otherwise I'll do it tonight after eating...