Adding ReadMe for using the gmfi_finder.py

…gistry into will

* Create Pham_Lee_2010.yml

This yml has the same problem with the gene model information:  I was able to confirm the relevance of two different IDs.  How should I assess which one is more useful?
I'm not confident about the confidence level I have listed.

* Update Pham_Lee_2010.yml

* Create Zhang_Burton_2008.yml

Another gene (SACPD-C) from the Zuo, Ikram paper.

* Update Zhang_Burton_2008.yml

* Update and rename Staygreen.yml to marlene/Staygreen.yml

* Rename marlene/Staygreen.yml to Glycine/max/wip_marlene/Staygreen.yml

* Rename Misc. fragments to Glycine/max/wip_marlene/Misc. fragments

* Update Pham_Lee_2010.yml

Attempting to make ymllint happy.

* Update Chen_Wang_2016.yml

Attempting to pacify ymllint.

* Update Pham_Lee_2010.yml

Still trying to satisfy ymllint.

* Update Misc. fragments

This is just stuff that I'm saving until I'm sure it's irrelevant.

* Update Zhou_Lakhssassi_2021.yml

Three seed-oil related genes from the Zuo, Ikram paper.

* Update Zhou_Lakhssassi_2021.yml

Three seed-oil content genes from Zuo, Ikram.

* Create Song_Li_2013.yml

This is one of the Zuo, Ikram genes but the authors of the only relevant study I can find only studied its effects in Arabidopsis.

* Create Ge_Yu_2016.yml

* Update Pham_Lee_2010.yml

Little changes to pacify ymllint.

* Update Chen_Wang_2016.yml

Little changes to satisfy ymllint.

* Update Chen_Wang_2016.yml

ymllint-inspired tweaks.

* Update Chen_Wang_2016.yml

Still trying to make ymllint happy.

* Create Tang_Su_2017.yml

Penultimate Zuo, Ikram gene.

* Update Tang_Su_2017.yml

Minor changes to make ymllint stop complaining.

* Create Zhang_Sun_2017.yml

The last of the Zuo, Ikram oil biosynthesis genes.

* Create Soyano_Hirakawa_2014_lotja.yml

LjNIN has positive and negative regulatory effect on its targets.  I think I've summarized them correctly, but I'd appreciate it if someone else would glance over these articles to make sure.

* Update Zhang_Sun_2017.yml

Minor ymllint-inspired alterations.

* Update Chen_Wang_2016.yml

Tiny changes for ymllint.

* Update Tang_Su_2017.yml

Tweaks for ymllint.

* Update Chen_Wang_2016.yml

Tweaks for ymllint.

* Update Pham_Lee_2010.yml

Tweaks for ymllint.

* Update Pham_Lee_2010.yml

Still trying to pacify ymllint.

* Update Tang_Su_2017.yml

Formatting changes for ymllint.

* Update Tang_Su_2017.yml

Fixing minor yml goofs.

* Update Chen_Wang_2016.yml

Formatting updates for ymllint.

* Create Indrasumunar_Searle_2012.yml

GmNFR1 is one of the nodulation genes discussed in Yang, Lan et. al., 2022.

* Create Cai_Wang_2017.yml

A group of genes from the Yang Lan paper.  In Yang Lan, the authors discuss the group as if it were one gene, but other papers indicate that it is a gene family.
(Is this too many trait ontologies?)

* Update and rename Misc. fragments to Delete_this

Remember to delete this.

* Create Song_Montez-Luz_2022.yml

Two nodulation-related genes from Yang Lan et. al.

* Create Searle_Men_2003.yml

One of the nodulation genes mentioned in Yang, Lan et. al., 2022.

* Update Staygreen.yml

* Update Searle_Men_2003.yml

* Create Wang_Wang_2014.yml

GmNNC1 is a gene mentioned in Yang, Lan et. al., 2022.

* Create Wang_Guo_2021.yml

The Yang Lan paper refers to STF4 as well as STF3, but there is no record of its existence in Soybase or GenBank.  Most papers treat them as a unit (STF3/4) with the same functions, so I have included STF3 but excluded STF4.  Should I make a separate entry for STF4?

* Create Yan_Wang_2018.yml

BEHL1 is a gene mentioned in Yang, Lan et. al. 2022.

* Update Searle_Men_2003.yml

Citation style update.

* Update Wang_Wang_2014.yml

Citation style update.

* Create Lu_Cheng_2020.yml

All of the gene_model_pub_names were very distant in Funnotate, but they are all supported by Soybase.

* Update Lu_Cheng_2020.yml

Tweaks for ymllint.

* Create Wang_Yang_2020.yml

* Create Zhuang_Xue_2021.yml

There is some ambiguity about the gene_model_pub_name.  I've noted the pros and cons of each option in the file.

* Added Glycine max Head_Galos_2012 for review

* Initial Commit of Wang_Lu_2022.traits.yml

* Change file name to Wang_Lu_2022.MtGSTF7.yml

* delete Wang_Lu_2022.traits.yml

…o their respective species directories (Lotus japonicus and Pisum sativum)