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ocimumSpecies dictionary is not generating output. #88

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ambarishK opened this issue Mar 3, 2019 · 4 comments
Open

ocimumSpecies dictionary is not generating output. #88

ambarishK opened this issue Mar 3, 2019 · 4 comments
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@petermr @ambarishK
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@ambarishK
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ambarishK commented Mar 3, 2019 •
edited

Sir, please try for the locally build ocimumSpecies.xml dictionary to get ocimum species informations.

I tried for the following command.

ambarish123@ubuntu:~$ ami-search-new -p osanctumnew/ --dictionary country /home/ambarish123/ocimumSpecies.xml
Run time log.
Generic values (AMISearchTool)
================================
basename            null
cproject            /home/ambarish123/osanctumnew
ctree               
cTreeList           20 trees [osanctumnew/PMC4238170, osanctumnew/PMC4286833, o
dryrun              false
excludeBase         null
excludeTrees        null
file types          []
forceMake           false
includeBase         null
includeTrees        null
log4j               
logfile             null
verbose             0

Specific values (AMISearchTool)
================================
dictionaryList       [country, /home/ambarish123/ocimumSpecies.xml]
dictionaryTop        null
dictionarySuffix     [xml]
ignorePlugins        []

cProject: osanctumnew
0    [main] DEBUG org.contentmine.ami.plugins.CommandProcessor  - running NORMA -i fulltext.xml -o scholarly.html --transform nlm2html --project osanctumnew
PMC4238170 .PMC4286833 PMC4296439 PMC4558530 PMC4562040 PMC4631451 PMC4774317 PMC4847459 PMC4945999 UNKNOWN nlm tag: issn-l
PMC4971952 PMC5061480 .PMC5234046 PMC5289091 PMC5301171 PMC5860693 PMC5891864 PMC5987647 PMC6023537 PMC6200556 PMC6239295 
running: word; word([frequencies])[{xpath:@count>20}, {w.stopwords:pmcstop.txt stopwords.txt}]......
running: search; search([country])[]......
running: search; search([/home/ambarish123/ocimumSpecies.xml])[]134330 [main] DEBUG org.contentmine.cproject.files.ResourceLocation  - FILE /home/ambarish123/ocimumSpecies.xml
......
create data tables
140368 [main] WARN  org.contentmine.ami.plugins.ResultsAnalysisImpl  - Null pluginOption
rrrrrrrr
issue:

Output file for the ocimumSpecies are empty and there is no cooccurrence between the search term. As per the used command, there would have been column for each search term
i.e country and ocimumSpecies but into the commonest.DataTables.html contains only column for country.

ocimumspecies_issue

ocimumSpecies dictionary
@ambarishK ambarishK added the help wanted Extra attention is needed label Mar 3, 2019
@petermr
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petermr commented Mar 3, 2019 via email

@ambarishK
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ambarishK commented Mar 3, 2019 •
edited

Yes sir. Even I will recreate the ocimum dictionary based on list of terms.

I splitted the ocimum2000 folder into four containing 500 articles into each and running for search results.

@ambarishK
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ambarishK commented Mar 4, 2019 •
edited

Sir, I created a new dictionary for Ocimum species using list of terms but result does not shows coverage for all entry terms into the dictionary.

command for creating dictionary.

ami-dictionary create --terms  "Ocimum africanum"  "Ocimum americanum" "Ocimum amicorum" "Ocimum andongense" "Ocimum angustifolium" "Ocimum angustilanceolatum" "Ocimum anisatum" "Ocimum anisodorum" "Ocimum anosurum" "Ocimum arborescens" "Ocimum aristatum" "Ocimum asperum" "Ocimum atrovirens" "Ocimum aureoglandulosum" "Ocimum auricula" "Ocimum balansae" "Ocimum barrelieri" "Ocimum basilicum" "Ocimum bullatum" "Ocimum burchellianum" "Ocimum caillei" "Ocimum calycosum" "Ocimum cameronii" "Ocimum campechianum" "Ocimum camporum" "Ocimum canescens" "Ocimum canum" "Ocimum capitatum" "Ocimum capitellatum" "Ocimum carnosum" "Ocimum caryophyllatum" "Ocimum caryophyllinum" "Ocimum centraliafricanum" "Ocimum chevalieri" "Ocimum ciliare" "Ocimum ciliatum" "Ocimum cinereum" "Ocimum circinatum" "Ocimum citriodorum" "Ocimum cochleatum" "Ocimum coddii" "Ocimum coetsa" "Ocimum coloratum" "Ocimum comigerum" "Ocimum comosum" "Ocimum congestum" "Ocimum cordifolium" "Ocimum crispum" "Ocimum cristatum" "Ocimum cuanzae" "Ocimum cufodontii" "Ocimum cyclophyllum" "Ocimum dalabaense" "Ocimum dambicola" "Ocimum decumbens" "Ocimum densiflorum" "Ocimum dentatum" "Ocimum depauperatum" "Ocimum descampsii" "Ocimum dhofarense" "Ocimum dichotomum" "Ocimum diffusum" "Ocimum dimidiatum" "Ocimum dinteri" "Ocimum dolomiticola" "Ocimum ebracteatum" "Ocimum ellenbeckii" "Ocimum elskensii" "Ocimum ericoides" "Ocimum exsul" "Ocimum falcatum" "Ocimum fastigiatum" "Ocimum febrifugum" "Ocimum filamentosum" "Ocimum filiforme" "Ocimum fimbriatum" "Ocimum fischeri" "Ocimum fissilabrum" "Ocimum flaccidum" "Ocimum fluminense" "Ocimum foetidum" "Ocimum formigense" "Ocimum formosum" "Ocimum forskolei" "Ocimum forsskaolii" "Ocimum frutescens" "Ocimum fruticosum" "Ocimum galpinii" "Ocimum glabrifolium" "Ocimum glaucum" "Ocimum glossophyllum" "Ocimum gracile" "Ocimum grandiflorum" "Ocimum gratissimum" "Ocimum graveolens" "Ocimum graveolens" "Ocimum guatemalense" "Ocimum guineense" "Ocimum hadiense" "Ocimum hanningtonii" "Ocimum hararense" "Ocimum hassleri" "Ocimum heckmannianum" "Ocimum helianthemifolium" "Ocimum heptodon" "Ocimum hians" "Ocimum hildebrandtii" "Ocimum hirsutissimum" "Ocimum hirsutum" "Ocimum hispidulum" "Ocimum holosericeum" "Ocimum homblei" "Ocimum huillense" "Ocimum incanescens" "Ocimum indicum" "Ocimum inflexum" "Ocimum inodorum" "Ocimum integerrimum" "Ocimum iringoense" "Ocimum irvinei" "Ocimum jamesii" "Ocimum johnstonii" "Ocimum kapiriense" "Ocimum katangense" "Ocimum kenyense" "Ocimum kilimandscharicum" "Ocimum knyanum" "Ocimum konianense" "Ocimum kunene" "Ocimum labiatum" "Ocimum lamiifolium" "Ocimum lanceolatum" "Ocimum laxiflorum" "Ocimum linearifolium" "Ocimum longistylum" "Ocimum macrostachyum" "Ocimum madagascariense" "Ocimum madagascariensis" "Ocimum majus" "Ocimum masaiense" "Ocimum maypurense" "Ocimum mearnsii" "Ocimum medium" "Ocimum membranaceum" "Ocimum menthifolium" "Ocimum menthoides" "Ocimum menyhartii" "Ocimum metallorum" "Ocimum micranthum" "Ocimum mildbraedii" "Ocimum minimum" "Ocimum minus" "Ocimum minutiflorum" "Ocimum mitwabense" "Ocimum modestum" "Ocimum mollissimum" "Ocimum monachorum" "Ocimum monadelphum" "Ocimum monocotyloides" "Ocimum monostachyum" "Ocimum montanum" "Ocimum montevideanum" "Ocimum moschatum" "Ocimum motjaneanum" "Ocimum nakurense" "Ocimum natalense" "Ocimum neumannii" "Ocimum neurophyllum" "Ocimum nigrum" "Ocimum nudicaule" "Ocimum nummularia" "Ocimum nutans" "Ocimum obovatum" "Ocimum obtusifolium" "Ocimum odontopetalum" "Ocimum odontosepalum" "Ocimum odorum" "Ocimum ovatum" "Ocimum paludosum" "Ocimum paniculatum" "Ocimum paniculatum" "Ocimum peltatum" "Ocimum petiolare" "Ocimum petitianum" "Ocimum peulhorum" "Ocimum piliferum" "Ocimum pilosum" "Ocimum plectranthus" "Ocimum poggeanum" "Ocimum polystachyon" "Ocimum procurrens" "Ocimum prostratum" "Ocimum pseudoserratum" "Ocimum pubescens" "Ocimum pumilum" "Ocimum punctatum" "Ocimum punctulatum" "Ocimum purpurascens" "Ocimum pyramidatum" "Ocimum racemosum" "Ocimum randii" "Ocimum rariflorum" "Ocimum rautanenii" "Ocimum reclinatum" "Ocimum reflexum" "Ocimum rigidum" "Ocimum ringoetii" "Ocimum robustum" "Ocimum roseoviolaceum" "Ocimum rothii" "Ocimum rotundifolium" "Ocimum rubicundum" "Ocimum rubrocostatum" "Ocimum rugosum" "Ocimum salinum" "Ocimum salvioides" "Ocimum sanctum" "Ocimum sassandrae" "Ocimum scabrum" "Ocimum schweinfurthii" "Ocimum scoparium" "Ocimum scutellarioides" "Ocimum selloi" "Ocimum sericeum" "Ocimum serpyllifolium" "Ocimum serpyllifolium" "Ocimum serratum" "Ocimum sideritidis" "Ocimum simile" "Ocimum simulans" "Ocimum siphonanthum" "Ocimum somaliense" "Ocimum spectabile" "Ocimum spicatum" "Ocimum stamineum" "Ocimum staminosum" "Ocimum stenoglossum" "Ocimum stirbeyi" "Ocimum striatum" "Ocimum stuhlmannii" "Ocimum suave" "Ocimum subserratum" "Ocimum suffrutescens" "Ocimum superbum" "Ocimum sylvaticum" "Ocimum tashiroi" "Ocimum tenellum" "Ocimum tenuiflorum" "Ocimum tereticaule" "Ocimum ternifolium" "Ocimum teucriifolium" "Ocimum thoningii" "Ocimum thonningii" "Ocimum thymiflorum" "Ocimum thymoides" "Ocimum thyrsiflorum" "Ocimum tomentosum" "Ocimum tomentosum" "Ocimum tomentosum" "Ocimum tortuosum" "Ocimum transamazonicum" "Ocimum trichodon" "Ocimum tuberosum" "Ocimum tubiforme" "Ocimum tweedieanum" "Ocimum urticifolium" "Ocimum urundense" "Ocimum usaramense" "Ocimum vaalae" "Ocimum vandenbrandei" "Ocimum vanderystii" "Ocimum verticillatum" "Ocimum verticillifolium" "Ocimum vihpyense" "Ocimum villosum" "Ocimum virgatum" "Ocimum viride" "Ocimum viridiflorum" "Ocimum viscosum" "Ocimum waterbergense" "Ocimum wilmsii" "Ocimum zatarhendi" "Ocimum zeylanicum" "Ocimum" "Tulsi" "Tulasi" "Thulsi" "Thulasi" "Basil" "Holy Basil" "Lemon basil" "Camphor basil" --dictionary oSpecies --outformats xml,html
ocimumSpecies
Snapshot of the ocimum species cooccurrence.

ocimumspeciessvg

Please resolve the issue.

@ambarishK
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As I observe using different dictionaries for Ocimum species, built-in dictionary for the species is sufficient to cover and report Ocimum species.

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