Dictionary Invasive_species - petermr/CEVOpen GitHub Wiki

Owner: Kanishka Parashar

Dictionary: Invasive_plant

Dictionary link:

Dictionary can be find here: https://github.com/petermr/CEVOpen/tree/master/dictionary/Invasive_species

Overview:

Dictionary Created: by using SPARQL query.
Motivation and goals: the motive is to create a dictionary containing information of plant invasive species across the globe, giving a brief description about the plant like- geographical location, synonyms etc. Further the dictionary content can be co-related to other dictionaries to extend the information and enhance knowledge such as- to find out the phytochemicals present in those plants and their effect.
What I did and why: At beginning I started studying about invasive plant their impact on the native plant. Then I downloaded a list of around 460 plant invasive species by using GISD database. Then I found wikidataID for each plant manually and created a sparql query to create a dictionary invasive_plant (Invasive_species). This was followed up by generating a minicorpora 'invasive' containing around 100 papers downloaded by using pygetpapers as tool. My later motive was to extract information from the downloaded plant.
What did not work (problems or hurdles i faced): Being new in the field of computational biology. I faced difficulty in running software and write commands to run them. But yes by the time, it became easy and comfortable to work.
What i hope to do: I aim to co- relate the invasive plant species with the chemical compound find in them.

Procedure:

Go to wikidata query page: https://query.wikidata.org/ and create SPARQL query.
Run SPARQL query using following command

## Selecting the prefered label
## Selecting the prefered label
SELECT Distinct * WHERE {
  VALUES ?item {
    wd:Q2086536 wd:Q190887 wd:Q310208 wd:Q1316058 wd:Q932729 wd:Q2701053 wd:Q2673511 wd:Q311430 wd:Q386585 wd:Q1621617 wd:Q2666767 wd:Q402385 wd:Q149401 wd:Q4672006 wd:Q136648 wd:Q15634290 wd:Q26745 wd:Q2717414 wd:Q2706362 wd:Q161246 wd:Q161115 wd:Q159221 wd:Q2732431 wd:Q4692133 wd:Q1949712 wd:Q159717 wd:Q27835 wd:Q159570 wd:Q1482093 wd:Q750307 wd:Q2717846 wd:Q1160961 wd:Q2834268 wd:Q160097 wd:Q156904 wd:Q2703227 wd:Q1472735 wd:Q3534965 wd:Q682164 wd:Q161568 wd:Q40051889 wd:Q309785 wd:Q4763286 wd:Q2353550 wd:Q275620 wd:Q848254 wd:Q311521 wd:Q2860589 wd:Q87594900 wd:Q163675 wd:Q2716675 wd:Q161114 wd:Q1816048 wd:Q28367 wd:Q311451 wd:Q5712311 wd:Q2875199 wd:Q1366575 wd:Q3219428 wd:Q6395156 wd:Q26158 wd:Q22111300 wd:Q426965 wd:Q158397 wd:Q814421 wd:Q2930211 wd:Q10944544 wd:Q162271 wd:Q4117077 wd:Q159066 wd:Q12345850 wd:Q164128 wd:Q161538 wd:Q2265513 wd:Q18461 wd:Q786072 wd:Q2720939 wd:Q26615 wd:Q163958 wd:Q163559 wd:Q158048 wd:Q12207493 wd:Q15547168 wd:Q1431280 wd:Q1368577 wd:Q1768699 wd:Q857220 wd:Q310961 wd:Q48996866 wd:Q2998776 wd:Q2943755 wd:Q163004 wd:Q259033 wd:Q2715047 wd:Q50840658 wd:Q4925284 wd:Q41530893 wd:Q41531244 wd:Q50840675 wd:Q15629297 wd:Q4115083 wd:Q848784 wd:Q2068262 wd:Q9311819 wd:Q36125 wd:Q289811 wd:Q2583146 wd:Q5114539 wd:Q577669 wd:Q164574 wd:Q158722 wd:Q27282 wd:Q341600 wd:Q21177 wd:Q1524349 wd:Q3281716 wd:Q160100 wd:Q2979028 wd:Q727330 wd:Q2712208 wd:Q5149520 wd:Q5152272 wd:Q19848765 wd:Q15248508 wd:Q5173212 wd:Q470109 wd:Q161406 wd:Q160221 wd:Q135531 wd:Q15397864 wd:Q3005741 wd:Q15528510 wd:Q687435 wd:Q5199880 wd:Q7186137 wd:Q41137071 wd:Q381584 wd:Q1391422 wd:Q145781 wd:Q5247707 wd:Q161735 wd:Q1157813 wd:Q2702202 wd:Q311432 wd:Q150385 wd:Q311239 wd:Q1196309 wd:Q15533996 wd:Q24192276 wd:Q21162077 wd:Q163649 wd:Q690645 wd:Q157969 wd:Q181318 wd:Q367242 wd:Q165403 wd:Q11126839 wd:Q33466 wd:Q159760 wd:Q549727 wd:Q1926297 wd:Q41505 wd:Q157726 wd:Q306504 wd:Q159331 wd:Q159331 wd:Q744339 wd:Q148882 wd:Q15597725 wd:Q15535258 wd:Q2740464 wd:Q621082 wd:Q5458608 wd:Q146684 wd:Q146136 wd:Q5494014 wd:Q164832 wd:Q164101 wd:Q3018415 wd:Q311194 wd:Q151046 wd:Q161879 wd:Q50380327 wd:Q50380330 wd:Q50410083 wd:Q1989614 wd:Q1634712 wd:Q847582 wd:Q1394846 wd:Q49550144 wd:Q376320 wd:Q3782768 wd:Q26354 wd:Q3926743 wd:Q1994229 wd:Q3926753 wd:Q3142116 wd:Q164149 wd:Q826602 wd:Q2716358 wd:Q20757547 wd:Q13919449 wd:Q931460 wd:Q2717256 wd:Q158110 wd:Q164091 wd:Q164181 wd:Q158913 wd:Q1661596 wd:Q158289 wd:Q47140799 wd:Q421057 wd:Q158035 wd:Q654064 wd:Q693409 wd:Q272754 wd:Q311175 wd:Q21175 wd:Q15504069 wd:Q11060111 wd:Q3163048 wd:Q148097 wd:Q822052 wd:Q311188 wd:Q311632 wd:Q6471912 wd:Q15345636 wd:Q332469 wd:Q15600070 wd:Q32465 wd:Q149265 wd:Q5364126 wd:Q35905 wd:Q15228001 wd:Q15228001 wd:Q1074201 wd:Q1848856 wd:Q3339674 wd:Q1768430 wd:Q157078 wd:Q10743709 wd:Q709649 wd:Q161083 wd:Q1076276 wd:Q29907 wd:Q15321400 wd:Q159413 wd:Q3338251 wd:Q5235063 wd:Q157513 wd:Q15129340 wd:Q1813408 wd:Q15227704 wd:Q162171 wd:Q158596 wd:Q6812536 wd:Q6820031 wd:Q6820033 wd:Q140905 wd:Q5699638 wd:Q2717688 wd:Q2719490 wd:Q2235813 wd:Q148532 wd:Q1073621 wd:Q158517 wd:Q15377318 wd:Q157307 wd:Q899338 wd:Q160407 wd:Q158130 wd:Q158875 wd:Q21310666 wd:Q20480616 wd:Q1040814 wd:Q13426501 wd:Q882908 wd:Q847939 wd:Q159743 wd:Q843726 wd:Q2355390 wd:Q15479065 wd:Q37083 wd:Q30166 wd:Q13936842 wd:Q310979 wd:Q144412 wd:Q311192 wd:Q141416 wd:Q162795 wd:Q7115068 wd:Q1640921 wd:Q15550928 wd:Q1209690 wd:Q3024698 wd:Q3595850 wd:Q3510828 wd:Q7142304 wd:Q7142302 wd:Q156790 wd:Q1766333 wd:Q3448230 wd:Q2068761 wd:Q135365 wd:Q42418587 wd:Q836721 wd:Q157419 wd:Q27657 wd:Q607380 wd:Q28557 wd:Q11090755 wd:Q3027867 wd:Q165227 wd:Q158468 wd:Q12024 wd:Q2900918 wd:Q271582 wd:Q3281616 wd:Q654001 wd:Q160343 wd:Q7199152 wd:Q15590374 wd:Q15247575 wd:Q4217123 wd:Q157571

  }
  SERVICE wikibase:label {
    bd:serviceParam wikibase:language "en".
    ?item rdfs:label ?itemLabel;
      skos:altLabel ?itemAltLabel;
      schema:description ?itemDescription.
}
  OPTIONAL {
    ?wikipedia schema:about ?item;
      schema:isPartOf <https://en.wikipedia.org/>.
  }
  OPTIONAL {
    ?hiwikipedia schema:about ?item;
      schema:isPartOf <https://hi.wikipedia.org/>.
  }
  OPTIONAL {
    ?tawikipedia schema:about ?item;
      schema:isPartOf <https://ta.wikipedia.org/>.
  }
  OPTIONAL {
    ?eswikipedia schema:about ?item;
      schema:isPartOf <https://es.wikipedia.org/>.
  }
  OPTIONAL {
    ?frwikipedia schema:about ?item;
      schema:isPartOf <https://fr.wikipedia.org/>.
  }
  OPTIONAL {
    ?dewikipedia schema:about ?item;
      schema:isPartOf <https://de.wikipedia.org/>.
  }
  OPTIONAL {
    ?zhwikipedia schema:about ?item;
      schema:isPartOf <https://zh.wikipedia.org/>.
  }
  OPTIONAL {
    ?urwikipedia schema:about ?item;
      schema:isPartOf <https://ur.wikipedia.org/>.
  }
  OPTIONAL { ?wikipedia wdt:P627 ?IUCN_taxon_ID. }
  OPTIONAL {  }
  OPTIONAL { ?wikipedia wdt:P225 ?taxon_name. }
  OPTIONAL { ?wikipedia wdt:P1843 ?taxon_common_name. }
}

After getting result download SPARQL endpoint from the link and get the SPARQL file.
Open SPARQL file in notepad
Use amidict for SPARQL mapping by the following command:

amidict -vv --dictionary invasive_plants --directory plantinvasivespecies --input sparql/sparql4 create --informat wikisparqlxml --sparqlmap wikidataURL=item,wikipediaPage=wikipedia,name=itemLabel,term=itemLabel,Description=itemDescription,_p627_iucn_taxonid=ICUN_taxon_ID,_p225_taxon_name=taxon_name,_p1843_taxon_common_name=t --transformName wikidataID=EXTRACT(wikidataURL,.*/(.*)) --synonyms=itemAltLabel

Commit changes in github.
Dictionary Invasive_plant has about 460 invasive plant entries.
Attributes in the dictionary are : WikidataID, WikidataURL, Description, Common name, plant IUCN status.

Shweata: Kanishka found GISD property in Wikidata. Here is a query I wrote to get plant invasive species using that property.

https://query.wikidata.org/#%23Cats%0ASELECT%20%3Fitem%20%3FitemLabel%20%3FGISD%20%3FGRIN%0AWHERE%20%0A%7B%0A%20%20%3Fitem%20wdt%3AP31%20wd%3AQ16521%20.%0A%20%20%3Fitem%20wdt%3AP105%20wd%3AQ7432%20.%0A%20%20%3Fitem%20wdt%3AP1421%20%3FGRIN%20.%0A%20%20%3Fitem%20wdt%3AP5626%20%3FGISD%20.%0A%20%20SERVICE%20wikibase%3Alabel%20%7B%20bd%3AserviceParam%20wikibase%3Alanguage%20%22%5BAUTO_LANGUAGE%5D%2Cen%22.%20%7D%0A%7D

GISD Database:

A list of around 460 plant invasive species was downloaded from the gisd database http://www.iucngisd.org/gisd/ . Mentioned species were then used to write a sparql query by manually finding their wikidataID.

Miniproject: Plant invasive species

The project includes developing a minicorpora 'invasive' that has around 100 paper downloaded by using 'pygetpapers' and creating sections of the downloaded paper by using 'ami'. Link to the minicorpora: https://github.com/petermr/CEVOpen/tree/master/minicorpora

Search_lib: this tool was developed to extract information from the created minicorpora.

Link to run search_lib and know more about it: https://github.com/petermr/openDiagram/wiki/Test-Report-for-Search_lib

ami_gui.py: this tool is developed to etract information present in the papers downloaded by using pygetpapers. The tools helps to retrieve information from the various sections of paper published.

the extracted data from the 'invasive' minicorpora of dictionary Invasive Species - https://drive.google.com/file/d/1gj5HFqptXdUvhOqj7C5Bz15CQHr_cohB/view?usp=sharing

ami search result data for the invasive_species dictionary and the country dictionary-

https://docs.google.com/spreadsheets/d/1P6qHaF7G05up0WDjzMC_wj9bDKlXCbMj/edit#gid=9874770

Currently, there are 187 Wikidata Items.