Mining crop literature for genes and enzyme products (terpenes)

Introduction

Among volatile organic compounds, plant terpenes account for a larger proportion and these terpenes are mainly synthesized by methylerythritol phosphate (MEP) and mevalonic acid (MVA) pathways. Terpene synthase (TPS) enzymes from these 2 pathways play a crucial role in modifying one terpene to another. Here, we attempt to collect and classify all TPS genes that are available from genomics studies. EC numbers and Wikidata IDs were also collected for them.

What does "Crops" repository contain

1. This "Crops" repository contain different folders named basing on crop name. Each of them contain README.md and excel file with TPS gene's information such as uniprot ID, uniprotkb ac/ID, Organism name, synonyms and corresponding TPS protein function etc.

2. DST-KARYA interns have also uploaded their crop specific dictionaries into respective folder.

3. DST-KARYA interns have created wikipages in this repository https://github.com/petermr/crops/wiki.

4. "TPS" folder created by Sagar Jadhav and it contains README and work on TPS enzyme collection.

5. "dictionaries" folder created by Sagar Jadhav and it contains README and xml dictionaries from 2020-2021.

6. "metadata analysis" folder created by Shweata Hegde and it contains README and metadata_analysis.py files.

7. "outreach" folder created by Shweata Hegde and contains InCOB and Wikidata Conference presentations

SUMMARY TABLE

Intern Name	Crop	Papers available (Research article)	Wikipage
Anam Anjum	Camellia Tomato	49 77	https://github.com/petermr/crops/blob/main/Solanum%20lycopersicum/eo_tomato.xml https://github.com/petermr/crops/blob/main/Camellia/eo_CAMSITps.xml
Anjali Shekhawat	Mentha	91	https://github.com/petermr/crops/blob/main/Mentha/eo_menthaTPS.xml
Prachi Singh	Zea mays	123	https://github.com/petermr/crops/blob/main/Zea%20mays/eo_ZeaTPS.xml
Rageshwari Singh	Vitis vinifera	163	https://github.com/petermr/crops/blob/main/Vitis/eo_VVinifera.xml
Shweata Hegde	metadata_analysis	TPS terms extraction from corpus	https://github.com/petermr/crops/tree/main/metadata_analysis
Sagar Jadhav	Combined above mini_tps dictionaries, Created tpsimage dictionary, Ran metadata analysis on 620 papers	crop tps dictionary, metadata analysis	https://github.com/petermr/crops/blob/main/dictinaries/crop_tpsenzyme.xml https://github.com/petermr/crops/blob/main/dictinaries/tpsimage.xml https://github.com/petermr/crops/blob/main/TPS%20sentences_full_search_result.csv

Important links

https://github.com/petermr/CEVOpen/wiki/crop5
https://github.com/petermr/openVirus/wiki/Documentation-of-getpapers-&-ami https://github.com/petermr/pygetpapers/blob/main/README.md
https://github.com/petermr/CEVOpen/wiki/GENE-:-TPS