KARYA Intern Projects

• Outlining projects for KARYA Interns
• Timeline: 8 weeks

TPS project

• Scoping exercise
• Whether there is enough systematic knowledge about TPS genes and enzymes or not
• List of TPS enzymes for a 5 plants

TO-DO for PMR, SJ, and SNH

• A guide to help them get started
• Tech?

Tasks

• Test the dictionaries (activity, compound, plant parts, plant, geolocation)
• Find terpene enzymes and their identifiers, related to their plants
• Standard corpus for each intern

INYAS Interns:

TPS genes for different species

Camellia

Oryza

Malus

Citrus

Mentha

Vitis

Zea

Crops	Number of TPS	Naming System
Camellia	73	CsTPS, CsTPS1, CsTPS2, ...CsTPS73
Mentha longifolia	63	MlongTPS, MlongTPS1, MlongTPS2, ...MlongTPS63
Citrus sinensis	54	CsTPS, CsTPS1, CsTPS2, ...CsTPS54
Zea mays	105	ZmTPS, ZmTPS1, ZmTPS2, ...ZmTPS105
Vitis vinifera	105	VvTPS, VviTPS, VvTPS1, VvTPS2, ...VvTPS105
Solanum lycopersicum	55	SlTPS, SlTPS1, SlTPS2, ...SlTPS55

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• Search papers/corpus "Zea mays terpene synthase" with https://europepmc.org/

  For eg.

  Query	Number of hits
  Zea mays terpene synthase	344
  Zea mays terpene synthase volatile	157
  Zea mays terpene synthase volatile TPS	66

• Create corpus

• Extract terms from papers.

• Create dictionary and test.

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Useful links:

• https://github.com/petermr/pygetpapers/blob/main/README.md

• https://github.com/petermr/openVirus/wiki/Documentation-of-getpapers-&-ami

• https://github.com/petermr/CEVOpen/wiki/GENE-:-TPS

• https://github.com/petermr/CEVOpen/wiki/Intern-Dictionaries

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Intern Name	Softwares installation	Crop	Papers available (Research article)	Wikipage
Anam Anjum, Ankit Lade	ami3, pygetpapers	Camellia Tomato	80 (49)	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, Anuv Chakraborty	ami3, pygetpapers	Mentha Citrus sinensis	145 (91)	32 bit system https://github.com/petermr/crops/blob/main/Mentha/eo_menthaTPS.xml
Prachi Singh, Prathmesh Sharma	ami3, pygetpapers	Zea mays	157 (123) metadata analysis	Testing error java https://github.com/petermr/crops/blob/main/Zea%20mays/eo_ZeaTPS.xml
Rageshwari Singh, Utkarsha Pande	ami3, pygetpapers	Vitis vinifera	211 (163)	https://github.com/petermr/crops/blob/main/Vitis%20vinifera/eo_VVinifera.xml
Anuv Chakraborty	ami3, pygetpapers	Citrus sinensis	metadata analysis	https://github.com/petermr/CEVOpen/wiki/Activities-Summary:-Anuv
Ankit Lade, Utkarsha Pande	ami3, pyami, pygetpapers	Solanum lycopersicum	metadata analysis	https://github.com/petermr/CEVOpen/wiki/Data-preprocessing-and-applying-Machine-learning-to-extract-information-from-the-papers
Utkarsha Pande	ami3, pygetpapers, pyami	Vitis vinifera	metadata analysis	https://github.com/petermr/CEVOpen/wiki/Installations-(pygetpapers-and-ami3)-on-macOS
		Rice

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TRAFFIC LIGHT

Intern Name	amidict	pygetpapers	docanalysis	pyami	metadata analysis	Wikipage
Ankit Lade	amidict	pygetpapers		pyami	metadata analysis	https://github.com/petermr/CEVOpen/wiki/Data-preprocessing-and-applying-Machine-learning-to-extract-information-from-the-papers
Anuv Chakraborty	amidict	pygetpapers				https://github.com/petermr/CEVOpen/wiki/Activities-Summary:-Anuv
Utkarsha Pande	amidict	pygetpapers		pyami	metadata analysis	https://github.com/petermr/CEVOpen/wiki/Installations-(pygetpapers-and-ami3)-on-macOS
Sagar Jadhav	amidict	pygetpapers		pyami	metadata analysis	https://github.com/petermr/CEVOpen/wiki/Smoke-test-for-Pyami ; https://github.com/petermr/CEVOpen/wiki/Scoping-through-TPS-Corpus