Synch #23
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Synch #23
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Adding ReadMe for using the gmfi_finder.py
* 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.
…o their respective species directories (Lotus japonicus and Pisum sativum)
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Trying to synch up Marlene and Main branches.