Dictionary Plant Secondary Metabolites - petermr/CEVOpen GitHub Wiki

Plant Secondary Metabolites DICTIONARY:

  1. I collected 3330 plant secondary metabolites and removed duplicates.

    TOTAL Secondary metabolites -3330

    WIKIDATA ID -1417

    NO WIKIDATA ID -1913

    Please, find dictionary. Presently, dictionary contain terms with 1417 WIKIDATA IDs

    Plant secondary metabolites dictionary

    Plant secondary metabolites version 1

  2. I used wikipedia page (https://en.wikipedia.org/wiki/Secondary_metabolite#Plant_secondary_metabolites) to find out only names of plant secondary metabolite classes. I also used following SPARQL queries

    SELECT ?instance_of ?instance_ofLabel WHERE {

    SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }

    ?instance_of wdt:P31 wd:Q11173.

    ?instance_of wdt:P31 **wd:Q331818**.}

    [ replacing wd:Q331818 (gibberellins) with wd:Q70702 (alkaloid ),

    wd:Q32528 (monoterpene), wd:Q80218 (sesquiterpene), wd:Q3234924 (isoflavonoid) and wd:Q222174 (flavonoid) ]

    Most of the Wikidata IDs were searched manually by searching papers.

  3. To get names of plant secondary metabolites, I also searched papers (supplementary data) of genome wide association studies of Arabidopsis and Rice as well as Tomato (Introgression Lines) (Alseekh et al., 2015; Matsuda et al., 2014; Wu et al., 2018).
    (https://academic.oup.com/plcell/article/27/3/485/6118131,

    https://www.pnas.org/content/110/50/20320,

    https://onlinelibrary.wiley.com/doi/10.1111/tpj.12681,

    https://doi.org/10.1016/j.molp.2017.08.012)

    Papers on secondary metabolites Papers on secondary metabolites

  4. Here, we are focusing on only PLANT SECONDARY METABOLITES.

  5. There are natural product databases available (Mangal et al., 2013; Tung 2014). I used database developed by Mangal et al., 2014. Some of the databases contain microbial natural products also and some require subscription and are not open access.

    I got database table from Tung 2014 paper

No. Database Reference
1. https://webs.iiitd.edu.in/raghava/npact/browse.php Mangal et al., 2013 working
2. http://alkamid.ugent.be/ Boonen et al., 2012 working
3. http://bif.uohyd.ac.in/nemedplant/ Meetei et al., 2012 working
4. http://kanaya.naist.jp/KNApSAcK_Family/ Takahashi et al., 2011 working
5. http://bioinformatics.charite.de/supernatural Dunkel et al., 2006 working
6. http://tcm.cmu.edu.tw/ Chen et al., 2011 working
7. http://cwtung.kmu.edu.tw/tipdb Lin et al., 2013 working
8. http://nubbe.iq.unesp.br/nubbeDB.html Valli et al., 2013 Not working
9. http://www.3dmet.dna.affrc.go.jp/ Maeda et al., 2013 Not working
10. http://www.ars-grin.gov/duke/ Duke and Bogenschutz Not working
11. http://www.megabionet.org/tcmid/ Xue et al., 2013 Not working
12. http://lifecenter.sgst.cn/hit/ Ye et al., 2011 Not working
13. http://www.hccbif.info/ Daisy et al., 2011 Not working
14. http://biolinfo.org/cmkb/ Gaikwad et al., 2008 Not working
15. http://tcm.cz3.nus.edu.sg/group/tcm-id/tcmid.asp Ji et al., 2006 Not working

  1. I have tested this dictionary on minicorpus of 10 papers. I used following commands.

    getpapers -q "plant secondary metabolites" -o secompoundMAP -x -p -k 10 -f corpora1/log.txt

    ami -p "secompoundMAP" section

    ami -p "secompoundMAP" search --dictionary secondary.xml

    It gave full data tables as

    plant secondary metabolites