style: change repo's name

[BenjaSanchez]

Description of the issue: The current name of the repository is too long and also redundant. We are about to make it public, and from the start it should have a memorable, short name. How about yeastGEM? Is it compliant with SysBio standards @demilappa @mihai-sysbio ? The model files already have that name, so it would be ideal :)

Of course more suggestions are welcomed @hongzhonglu @feiranl @zhengmingzhu @edkerk @simas232

[edkerk]

The Sysbio standard would be Saccharomyces_cerevisiae-GEM. Any explicit problems with too long repository name?

[BenjaSanchez]

@edkerk no problems in terms of functionality, but it's hard to remember/google/type/say. Overall unpractical, in my opinion. The yeast consensus model is already known in the community as "yeast7", "yeast6", etc., so I think it should remain with the word "yeast" in it, with my respects to other yeasts @edkerk @simas232 @IVANDOMENZAIN

[hongzhonglu]

@BenjaSanchez @edkerk Can it be S.cerevisiae-GEM_Yeast8 so that it is to be known?

[BenjaSanchez]

@hongzhonglu the number "8" should not be in the repo because the version will change in the future (Yeast9, Yeast10, etc.)

[IVANDOMENZAIN]

What about Saccharomyces_cerevisiae-yeastGEM? Still a long name but its close to the Sysbio standard and also keeps the yeastGEM string for making it accesible from search engines.

[BenjaSanchez]

@IVANDOMENZAIN it becomes even longer, so also not ideal. @mihai-sysbio @demilappa any thoughts? I also think that maybe we should rethink the standard Latin_name-GEM as in my opinion is not practical at all for repository names. Maybe just the KEGG code, like sceGEM, yliGEM, kmxGEM, scoGEM, etc? Could we start the discussion somewhere else maybe? @SysBioChalmers/everyone

[mihai-sysbio]

The way I see it, the name should be composed of 3 elements:

• a common/short identifier for people to call it by: yeast
• a specific identifier, for accuracy: currently Latin-name, but how about using DNA barcoding as a global standard for species identification http://www.boldsystems.org - fewer characters?
• a tag useful for search and integration with other systems: -GEM

[haowang-bioinfo]

It might be unnecessary to standardize everything. In this particular case, yeastGEM looks good.

[hongzhonglu]

@Hao-Chalmers @BenjaSanchez I agree. yeastGEM is easy to remember and communicate.

[BenjaSanchez]

@mihai-sysbio then maybe just yeast-GEM? I think in this case history ends up being more important than standardization, similar to this we are not changing the name of HMR to Homo_sapiens-GEM I suppose...

[mihai-sysbio]

yeast-GEM does 2/3 of the job. For the last bit, how about we have the full latin name in both the readme (it's there) and repo description (also there but it's abbreviated)?

[BenjaSanchez]

@mihai-sysbio works for me :)

[BenjaSanchez]

@mihai-sysbio I have updated the readme to highlight the latin name in the title, see PR #86. Also in the repo description. Let me know if anything else should be included.

[mihai-sysbio]

I've been talking to @Hao-Chalmers that we could set the standard to common_name-GEM for the important model organisms that have one, see https://en.wikipedia.org/wiki/Model_organism#Selected_model_organisms . On that list there is:

Schizosaccharomyces pombe, also called “fission yeast”, is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology.

Using yeast-GEM becomes vague all of a sudden.

[BenjaSanchez]

@mihai-sysbio @Hao-Chalmers S. pombe might be a model organism in vitro but in terms of modeling is not much that has been done compared to S. cerevisiae... again, I think that models that are already known to the community (and published) such as yeast and HMR should not change name too much, otherwise it just confuses users. If we have to change then I would rather do it to something short like @feiranl suggests: sce-GEM

[BenjaSanchez]

@mihai-sysbio case in point: https://github.com/SysBioChalmers/HMR3-GEM

can we proceed then with yeast-GEM? We are just waiting for this to go public... if needed we can discuss in person @edkerk @mihai-sysbio @demilappa :)

[edkerk]

I support both yeast-GEM and sce-GEM with preference for the first. Most people will think S. cereivisae when they read yeast, and any further confusion is avoided by clearly stating the latin name in the repository header, README, etc.

Let's settle this and move on :)

[mihai-sysbio]

Summary for future reference: GEM repo names have to be comfortable, scientific and practical. Obviously they can't be all at the same time; priority is given to comfort and practicality. So, all GEM repos should be named common_name, Latin_name, or keggid followed by -GEM, whatever is considered most adequate by the repo admin. For the sake of convention/science, there will be a centralized place (web page) that will contain all the required info for all our models, with a link to each Github repo. Alternatively, we could have a url-shortener style of redirect. A solution for this scientific naming purpose will be decided together.

For this repo, the new name is yeast-GEM.