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petermr / quantumchem

searching Open Access literature for quantum chemistry (inspiration Leonie Mueck)
Apache License 2.0
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run `ami-search` on sample `qchem` #5

Open petermr opened 5 years ago

petermr commented 5 years ago

Tested ami-search on subset qchem100 with program dictionary (of computational codes).

MacBook-Pro-3:quantumchem pm286$ ami-search  -p qchem100/ --dictionary country funders dictionary/program.xml 

Generic values (AMISearchTool)
================================
-v to see generic values
oldstyle            true

Specific values (AMISearchTool)
================================
oldstyle             true
strip numbers        false
wordCountRange       (20,1000000)
wordLengthRange      (1,20)

dictionaryList       [country, funders, dictionary/program.xml]
dictionaryTop        null
dictionarySuffix     [xml]

0    [main] DEBUG org.contentmine.ami.tools.AbstractAMISearchTool  - old style search command); change
cProject: qchem100
legacy cmd> word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt
legacy cmd> search(country)
legacy cmd> search(funders)
legacy cmd> search(dictionary/program.xml)
PMC3014667 .PMC3206452 PMC3734700 PMC3908927 PMC3961104 PMC3962182 PMC3969289 !PMC3982559 PMC4171759 PMC4194464 !PMC4236287 .PMC4322582 PMC4489505 PMC4560430 PMC4827478 PMC4914947 PMC5073744 PMC5378044 PMC5446292 PMC5633641 PMC5698732 .PMC5789983 PMC5811152 PMC5956981 PMC5968443 PMC6019389 PMC6036964 PMC6126658 PMC6218094 PMC6236472 PMC6314872 .PMC6346626 PMC6356090 PMC6409624 PMC6409765 PMC6438353 PMC6465357 PMC6470247 PMC6477054 PMC6479474 PMC6480351 .PMC6515988 PMC6517537 PMC6523831 PMC6527782 PMC6527900 PMC6535778 PMC6540877 PMC6544456 PMC6545332 PMC6547729 .PMC6548831 PMC6551249 PMC6553010 PMC6562893 PMC6565634 PMC6566378 PMC6568047 PMC6588603 PMC6604737 PMC6604742 .PMC6610095 PMC6614426 PMC6616327 PMC6617658 PMC6620477 PMC6625489 PMC6625822 PMC6630283 PMC6630582 PMC6632042 .PMC6637141 PMC6640208 PMC6641944 PMC6642191 PMC6644248 PMC6646311 PMC6646321 PMC6650822 PMC6651270 PMC6651417 .PMC6659639 PMC6659707 PMC6661861 PMC6662765 PMC6664395 PMC6667904 PMC6668418 PMC6669735 PMC6677555 PMC6678672 .PMC6680743 PMC6683176 PMC6689020 PMC6690562 !PMC6691062 PMC6694198 PMC6697675 PMC6700155 PMC6704071 PMC3014667 .PMC3206452 
large document (1091) for PMC3206452 truncated to 500 sections
PMC3734700 PMC3908927 PMC3961104 PMC3962182 PMC3969289 PMC3982559 1451 [main] DEBUG org.contentmine.ami.plugins.word.WordCollectionFactory  - no words found to extract
PMC4171759 PMC4194464 PMC4236287 1621 [main] DEBUG org.contentmine.ami.plugins.word.WordCollectionFactory  - no words found to extract
.PMC4322582 PMC4489505 PMC4560430 PMC4827478 PMC4914947 PMC5073744 PMC5378044 PMC5446292 PMC5633641 PMC5698732 .PMC5789983 PMC5811152 PMC5956981 PMC5968443 PMC6019389 PMC6036964 PMC6126658 PMC6218094 PMC6236472 PMC6314872 .PMC6346626 PMC6356090 PMC6409624 PMC6409765 PMC6438353 PMC6465357 PMC6470247 PMC6477054 PMC6479474 PMC6480351 .PMC6515988 PMC6517537 PMC6523831 PMC6527782 PMC6527900 PMC6535778 PMC6540877 PMC6544456 PMC6545332 PMC6547729 .PMC6548831 PMC6551249 PMC6553010 PMC6562893 PMC6565634 PMC6566378 PMC6568047 PMC6588603 PMC6604737 PMC6604742 .PMC6610095 PMC6614426 PMC6616327 PMC6617658 PMC6620477 PMC6625489 PMC6625822 PMC6630283 PMC6630582 PMC6632042 .PMC6637141 PMC6640208 PMC6641944 PMC6642191 PMC6644248 PMC6646311 PMC6646321 PMC6650822 PMC6651270 PMC6651417 .PMC6659639 PMC6659707 PMC6661861 PMC6662765 PMC6664395 PMC6667904 PMC6668418 PMC6669735 PMC6677555 PMC6678672 .PMC6680743 PMC6683176 PMC6689020 PMC6690562 PMC6691062 4974 [main] DEBUG org.contentmine.ami.plugins.word.WordCollectionFactory  - no words found to extract
PMC6694198 PMC6697675 PMC6700155 PMC6704071 .....................
large document (1091) for PMC3206452 truncated to 500 sections
..............................
large document (1091) for PMC3206452 truncated to 500 sections
.............................12011 [main] DEBUG org.contentmine.cproject.files.ResourceLocation  - FILE /Users/pm286/workspace/projects/quantumchem/dictionary/program.xml
.
large document (1091) for PMC3206452 truncated to 500 sections
.............................
create data tables
14645 [main] WARN  org.contentmine.ami.plugins.ResultsAnalysisImpl  - Null pluginOption
rrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrrMacBook-Pro-3:quantumchem pm286$

Explore if the data tables reflect what is in the text.