KARYA Intern Projects - petermr/CEVOpen GitHub Wiki

  • 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

  • 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.

Useful links:

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

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
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