from __future__ import unicode_literals
import json
import numpy as np
import pandas as pd
from pandas import DataFrame, Series
with open('biotech500.json', 'rb') as fp:
data = json.load(fp)
print data.keys()
print data['response'].keys()
[u'response'] [u'start', u'maxScore', u'numFound', u'docs']
len(data['response']['docs'])
500
print data['response']['docs'][0].keys()
[u'journal', u'article_type', u'score', u'publication_date', u'eissn', u'id']
for k in data['response']['docs'][0].keys():
print data['response']['docs'][0][k], type(data['response']['docs'][0][k])
PLoS ONE <type 'unicode'> Research Article <type 'unicode'> 1.2119352 <type 'float'> 2014-01-29T00:00:00Z <type 'unicode'> 1932-6203 <type 'unicode'> 10.1371/journal.pone.0086174/title <type 'unicode'>
articles_list = data['response']['docs']
articles = DataFrame(articles_list)
articles.head()
abstract | article_type | author_display | eissn | id | journal | publication_date | score | title_display | |
---|---|---|---|---|---|---|---|---|---|
0 | NaN | Research Article | NaN | 1932-6203 | 10.1371/journal.pone.0086174/title | PLoS ONE | 2014-01-29T00:00:00Z | 1.211935 | NaN |
1 | NaN | Research Article | NaN | 1932-6203 | 10.1371/journal.pone.0086174/abstract | PLoS ONE | 2014-01-29T00:00:00Z | 1.211935 | NaN |
2 | NaN | Research Article | NaN | 1932-6203 | 10.1371/journal.pone.0086174/references | PLoS ONE | 2014-01-29T00:00:00Z | 1.211935 | NaN |
3 | NaN | Research Article | NaN | 1932-6203 | 10.1371/journal.pone.0086174/body | PLoS ONE | 2014-01-29T00:00:00Z | 1.211935 | NaN |
4 | NaN | Research Article | NaN | 1932-6203 | 10.1371/journal.pone.0086174/introduction | PLoS ONE | 2014-01-29T00:00:00Z | 1.211935 | NaN |
5 rows × 9 columns
# We got more abstracts this time.
articles = articles[articles['abstract'].notnull()]
print len(articles)
articles.head()
60
abstract | article_type | author_display | eissn | id | journal | publication_date | score | title_display | |
---|---|---|---|---|---|---|---|---|---|
7 | [\nThe objective of this paper is to assess th... | Research Article | [Latifah Amin, Md. Abul Kalam Azad, Mohd Hanaf... | 1932-6203 | 10.1371/journal.pone.0086174 | PLoS ONE | 2014-01-29T00:00:00Z | 1.211935 | Determinants of Public Attitudes to Geneticall... |
16 | [\n Atrazine (ATZ) and S-metolachlor (S... | Research Article | [Cristina A. Viegas, Catarina Costa, Sandra An... | 1932-6203 | 10.1371/journal.pone.0037140 | PLoS ONE | 2012-05-15T00:00:00Z | 1.119538 | Does <i>S</i>-Metolachlor Affect the Performan... |
17 | [\nDue to environmental persistence and biotox... | Research Article | [Yonggang Yang, Meiying Xu, Zhili He, Jun Guo,... | 1932-6203 | 10.1371/journal.pone.0070686 | PLoS ONE | 2013-08-05T00:00:00Z | 1.119538 | Microbial Electricity Generation Enhances Deca... |
34 | [\n Intensive use of chlorpyrifos has r... | Research Article | [Shaohua Chen, Chenglan Liu, Chuyan Peng, Hong... | 1932-6203 | 10.1371/journal.pone.0047205 | NaN | 2012-10-08T00:00:00Z | 1.119538 | Biodegradation of Chlorpyrifos and Its Hydroly... |
35 | [Background: The complex characteristics and u... | Research Article | [Zhongbo Zhou, Fangang Meng, So-Ryong Chae, Gu... | 1932-6203 | 10.1371/journal.pone.0042270 | NaN | 2012-08-09T00:00:00Z | 0.989541 | Microbial Transformation of Biomacromolecules ... |
5 rows × 9 columns
# Abstracts and authors are lists
print type(articles.ix[7,0]), len(articles.ix[7,0])
print type(articles.ix[7,2]), len(articles.ix[7,2])
DataFrame([articles.abstract.apply(len), articles.author_display.apply(len)])
<type 'list'> 1 <type 'list'> 4
7 | 16 | 17 | 34 | 35 | 43 | 58 | 59 | 66 | 79 | 82 | 91 | 100 | 106 | 115 | 131 | 132 | 141 | 158 | 161 | ||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
abstract | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | ... |
author_display | 4 | 6 | 6 | 6 | 8 | 3 | 2 | 24 | 7 | 7 | 3 | 11 | 2 | 8 | 3 | 4 | 3 | 8 | 6 | 11 | ... |
2 rows × 60 columns
# Are they all from PLoS ONE? ... We can tell by eISSN == 1932-6203
# ... http://www.plosone.org/static/information.action
len(articles[articles.eissn == '1932-6203'])
54
# If we care, we can fill in the missing journals based on the eISSN.
articles[articles.eissn != '1932-6203'].ix[:,['eissn', 'journal']]
eissn | journal | |
---|---|---|
100 | 1545-7885 | PLoS Biology |
193 | 1549-1676 | PLoS Medicine |
208 | 1549-1676 | PLoS Medicine |
230 | 1549-1676 | NaN |
235 | 1549-1676 | PLoS Medicine |
240 | 1549-1676 | PLoS Medicine |
6 rows × 2 columns
import nltk
from nltk.corpus import stopwords
import string
# Globally define a set of stopwords. We can add sciency stuff to it as well.
stops = set(stopwords.words('english'))
stops.add('conclusions') # just an example
def wordify(abs_list):
'''Take the abstract field from PLoS API and convert it to a filtered list of words.'''
# Make it a string.
text = ' '.join(abs_list).strip(' \n')
if text == '':
return np.nan
else:
# Remove punctuation & replace with space,
# because we want 'metal-contaminated' => 'metal contaminated'
# ...not 'metalcontaminated', and so on.
for c in string.punctuation:
text = text.replace(c, ' ')
# Now make it a Series of words, and do some cleaning.
words = Series(text.split(' '))
# aseries.apply(lambda s: s.strip()) # should be unnecessary: split should already do this.
words = words.str.lower()
words = words[words.str.len() > 1]
words = words[~words.str.contains(r'[^#@a-z]')] # What exactly does this do?
# Filter globally-defined stopwords
ignore = stops & set(words.unique())
words_out = [w for w in words.tolist() if w not in ignore]
return words_out
# Test
test_abstract = articles.ix[16, 0]
wordify(test_abstract)
[u'atrazine', u'atz', u'metolachlor', u'met', u'two', u'herbicides', u'widely', u'used', u'often', u'mixtures', u'present', u'work', u'examined', u'whether', u'presence', u'met', u'affects', u'atz', u'biodegradation', u'activity', u'bioaugmentation', u'bacterium', u'pseudomonas', u'sp', u'strain', u'adp', u'crop', u'soil', u'met', u'concentrations', u'selected', u'relevance', u'worst', u'case', u'scenarios', u'soil', u'contamination', u'commercial', u'formulation', u'containing', u'herbicides', u'concentrations', u'representative', u'application', u'high', u'doses', u'formulation', u'soil', u'corresponding', u'dose', u'approximately', u'higher', u'recommended', u'field', u'dose', u'rd', u'presence', u'pure', u'met', u'significantly', u'affected', u'neither', u'bacteria', u'survival', u'initial', u'viable', u'cells', u'soil', u'atz', u'mineralization', u'activity', u'consistently', u'biodegradation', u'experiments', u'larger', u'soil', u'microcosms', u'spiked', u'double', u'formulation', u'inoculated', u'bacterium', u'revealed', u'atz', u'rapidly', u'days', u'extensively', u'removed', u'soil', u'days', u'concentration', u'met', u'decreased', u'moderately', u'initial', u'inoculated', u'non', u'inoculated', u'microcosms', u'concomitantly', u'accumulation', u'two', u'metabolites', u'met', u'ethanesulfonic', u'acid', u'met', u'oxanilic', u'acid', u'found', u'despite', u'dissipation', u'almost', u'atz', u'treated', u'soils', u'respective', u'eluates', u'still', u'highly', u'toxic', u'aquatic', u'microalgae', u'species', u'toxic', u'untreated', u'soil', u'suggest', u'high', u'toxicity', u'may', u'due', u'met', u'metabolites', u'remaining', u'soil']
articles['words'] = articles.apply(lambda s: wordify(s['abstract'] + [s['title_display']]), axis=1)
articles.drop(['article_type', 'score', 'title_display', 'abstract'], axis=1, inplace=True)
articles.head()
author_display | eissn | id | journal | publication_date | words | |
---|---|---|---|---|---|---|
7 | [Latifah Amin, Md. Abul Kalam Azad, Mohd Hanaf... | 1932-6203 | 10.1371/journal.pone.0086174 | PLoS ONE | 2014-01-29T00:00:00Z | [objective, paper, assess, attitude, malaysian... |
16 | [Cristina A. Viegas, Catarina Costa, Sandra An... | 1932-6203 | 10.1371/journal.pone.0037140 | PLoS ONE | 2012-05-15T00:00:00Z | [atrazine, atz, metolachlor, met, two, herbici... |
17 | [Yonggang Yang, Meiying Xu, Zhili He, Jun Guo,... | 1932-6203 | 10.1371/journal.pone.0070686 | PLoS ONE | 2013-08-05T00:00:00Z | [due, environmental, persistence, biotoxicity,... |
34 | [Shaohua Chen, Chenglan Liu, Chuyan Peng, Hong... | 1932-6203 | 10.1371/journal.pone.0047205 | NaN | 2012-10-08T00:00:00Z | [intensive, use, chlorpyrifos, resulted, ubiqu... |
35 | [Zhongbo Zhou, Fangang Meng, So-Ryong Chae, Gu... | 1932-6203 | 10.1371/journal.pone.0042270 | NaN | 2012-08-09T00:00:00Z | [background, complex, characteristics, unclear... |
5 rows × 6 columns
I substituted the variables Colin used with the data derived from the articles
DF.
If we use this method, it might be better to rewrite the NLP and cloud-generating code such that we are not interconverting among data structures so frequently (DF, list, string, ...).
abs_df = DataFrame(articles['words'].apply(lambda x: ' '.join(x)).tolist(), columns=['text'])
abs_df.head()
text | |
---|---|
0 | objective paper assess attitude malaysian stak... |
1 | atrazine atz metolachlor met two herbicides wi... |
2 | due environmental persistence biotoxicity poly... |
3 | intensive use chlorpyrifos resulted ubiquitous... |
4 | background complex characteristics unclear bio... |
5 rows × 1 columns
abs_set_df = DataFrame(articles['words'].apply(lambda x: ' '.join(set(x))).tolist(), columns=['text'])
abs_set_df.head()
text | |
---|---|
0 | among developed attitude paper identify accept... |
1 | aquatic mineralization dose experiments still ... |
2 | mfc hypothesized distinctly results nitrogen s... |
3 | fungal contaminant tcp accumulative gc morphol... |
4 | origin humic mineralization show mainly result... |
5 rows × 1 columns
This section uses all words from abstracts to find the common word pairs.
#include all words from abstracts for getting common word pairs
words_all = pd.Series(' '.join(abs_df['text']).split(' '))
words_all.value_counts()
study 56 using 33 two 32 patients 31 biodegradation 30 non 29 data 28 three 28 analysis 27 compared 27 soil 27 new 27 results 26 species 25 cell 25 ... engage 1 thermal 1 geochip 1 dominant 1 suggests 1 third 1 usually 1 locomotion 1 rpos 1 scales 1 prefer 1 quite 1 protocatechuate 1 routine 1 agr 1 Length: 3028, dtype: int64
relevant_words_pairs = words_all.copy()#.str.lower()
#relevant_words_pairs = relevant_words_pairs[~relevant_words_pairs.str.contains(r'[^#@a-z]')]
#relevant_words_pairs = relevant_words_pairs[relevant_words_pairs.str.len() > 1]
#ignore = set(stopwords.words('english')) & set(relevant_words_pairs.unique())
relevant_words_pairs.value_counts()#.drop(ignore)
study 56 using 33 two 32 patients 31 biodegradation 30 non 29 data 28 three 28 analysis 27 compared 27 soil 27 new 27 results 26 species 25 cell 25 ... engage 1 thermal 1 geochip 1 dominant 1 suggests 1 third 1 usually 1 locomotion 1 rpos 1 scales 1 prefer 1 quite 1 protocatechuate 1 routine 1 agr 1 Length: 3028, dtype: int64
from nltk.collocations import BigramCollocationFinder
from nltk.metrics import BigramAssocMeasures
bcf = BigramCollocationFinder.from_words(relevant_words_pairs)
for pair in bcf.nbest(BigramAssocMeasures.likelihood_ratio, 30):
print ' '.join(pair)
synthetic biology spider silk es cell adjacent segment medical imaging dp dtmax security privacy industry backgrounds removal initiation uv irradiated gm salmon persistent crsab antimicrobial therapy limb amputation cellular phone wireless powered minimally invasive phone technology heavy metals battery powered composite mesh frequency currents genetically modified tissue engineering catheter removal acting reversible brassica napus brown streak quasi stiffness data code
#these are the most common paired words
bcf.nbest(BigramAssocMeasures.likelihood_ratio, 20)
[(u'synthetic', u'biology'), (u'spider', u'silk'), (u'es', u'cell'), (u'adjacent', u'segment'), (u'medical', u'imaging'), (u'dp', u'dtmax'), (u'security', u'privacy'), (u'industry', u'backgrounds'), (u'removal', u'initiation'), (u'uv', u'irradiated'), (u'gm', u'salmon'), (u'persistent', u'crsab'), (u'antimicrobial', u'therapy'), (u'limb', u'amputation'), (u'cellular', u'phone'), (u'wireless', u'powered'), (u'minimally', u'invasive'), (u'phone', u'technology'), (u'heavy', u'metals'), (u'battery', u'powered')]
This takes only unique words from each abstract.
#following http://nbviewer.ipython.org/github/sanand0/ipython-notebooks/blob/master/Text-analysis.ipynb
#only includes a set() of words from each abstract
words = pd.Series(' '.join(abs_set_df['text']).split(' '))
words.value_counts()
study 38 two 23 using 21 results 20 three 20 analysis 20 compared 17 used 16 higher 16 may 16 non 15 based 15 significantly 14 also 14 however 14 ... septal 1 recommendations 1 genomes 1 poking 1 gck 1 optimised 1 varied 1 counting 1 monitoring 1 malware 1 tmc 1 rape 1 occur 1 conversely 1 cda 1 Length: 3028, dtype: int64
That was done in the function wordify()
top_words = words.value_counts().reset_index()
top_words.columns = ['word', 'count']
top_words.head(15)
word | count | |
---|---|---|
0 | study | 38 |
1 | two | 23 |
2 | using | 21 |
3 | results | 20 |
4 | three | 20 |
5 | analysis | 20 |
6 | compared | 17 |
7 | used | 16 |
8 | higher | 16 |
9 | may | 16 |
10 | non | 15 |
11 | based | 15 |
12 | significantly | 14 |
13 | also | 14 |
14 | however | 14 |
15 rows × 2 columns
word_list = list(top_words.word)
word_str = ' '.join(word_list)
print word_str
study two using results three analysis compared used higher may non based significantly also however present methods rate well respectively associated model new time gene suggest background high important one data found showed process potential biodegradation performance development activity degradation enhanced could aim lower genes presence different species bioremediation major days available use devices revealed determine environmental studies type increased engineering method growth including level significant demonstrated specific observed due objective biological within following increase whether patient provide genetically cell protein medical research identified device patients health current applications public tissue transgenic evidence possible materials findings ability molecular improve long conducted small efficient identify large rates engineered quality clinical design information concentrations controls reduce selected number methodology impact developed work among derived control common affect demonstrate years novel application soil assessed expression strain role order analyses natural term treated environment designed techniques microbial biomass soils period resistance selection outcomes first inoculated candidates trials field carbon waste surface wild make ph reduced cellular measured incidence included follow performed synthetic system addition six characteristics needed animal essential optimal independent treatment generation primary concentration thus factors involved particularly products technologies commercial relative changes greater function evaluate cells systems furthermore relevant uptake better excellent remain towards known culture effective introduce support many contaminated proteins ci exposure point genetic article vs strains life influence recent response implant conditions models multi according adhesion pcr often plants failure appropriate samples strategies approach without regulation improvement would help dna initial processes reduction production bacteria effects morphology network correlation show surgery behavior highly moreover sources tested effect least alternative mainly prosthetic interactions per body central randomized criteria native report biomaterial nature bacterial describe general frequency determined risks factor shown enzyme therefore functional established regulatory sp lines allow approximately little mechanisms modified provided obtained lead outcome animals understanding biology water electron future evaluating persistent values half desired critical material environments introduction degrade accumulation transformation low contamination day invasive address useful example region co benefit still genome networks platform larger wt requires test technical regeneration isolate minimal result indicated metals measurement heart making case scanning countries respect reference pollutant toxic achieved significance microscopy formed ii whereas likely overexpression screening 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standard induction human success mutants activities reported differences resulted component science ranged levels difference power provides contrast formation capable fate contacts scaffolds previously increasing removed readily vivo risk confirmed comparing pollutants issue rapid energy become month either facilities us crucial controlled implemented structure assess much form grow anterior studied followed conclusion step directly synthesis meet cultured specifically reports real employed consistently additional area rat dioxygenase wastes polycyclic full red experiment cause part although accumulate comparison reductase fold supplies completely toward genus organisms implantable supplied types circuitry inductive regulator place qrt perspective processed supply predict post multiple cultures modern appeared verified intense index loads height practice week proposed generate marine nerve industrial remained investments regardless conserved published acceptance demonstrates 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antiarrhythmic cleanup injectables dissemination connected inadequate mycobacterium accentuated strongly reusing display rather spectrometry pooled lignin catalyzes converted efforts interventional al causing exoskeletal beats illinois storage internet ge define anaerobic hospitals stainings commentators providers formulation peptide periods notion reliability chains necessitating sirna kingdom prediction divergence msc nd latest dimension germination biosciences patterns capsules quinone microbes programmable promoted sport increasingly displays tracking domestic metolachlor testing events ratios untested differentiation estimation predicts default details underlying batteries dose tcp obtain center relies expressing determinants document facepiece geographical signal oligomeric adverse surveillance administration proper began media diets proto productivity anchored infer cmd diabetes status mosaic organized mfc chimeric discouraged intended decabromodiphenyl structurally reporting acda strengths contraception extended cladosporium olfactory weekly dimethoxyphenol adw cardiopulmonary find exposed classical chromatopraphy governance poly accessible carboxylate works negative dense neurologic annually methodological metabolite underwent kda endocardial competition tme pioneer uraninite cumene markers dysphonia infection harbors colloidal achieves characterization organizing tetramer home bioenergy qualitative nutrients strikingly necessary tests resolved stakeholders match plos utility attractive add arrest dyes pcl pups adp context measuring fluctuating dimers government semi heteroresistance loss diffraction transmits connective cerevisiae receptor biologists preference novosphingobium increases dark tendon bioreactor white evoked convention absolute agr interact effluents serious phone sectors detecting dsrna bioethical rescued potato longer restrained smp bibliographies healthy code dissipation edk monogastric parafac disorders nanopod inverse prospectively bioconcentration kate adjustment biphenyl gc themes existing global monsanto neuroscience transform abdominal tufa pbdes green loosening quarters tentative epidemiological hemodynamic ni constructed neoformed discovery collections adversely tomography barriers preventing setting text degenerative assayed symptomatic update problems continue beneficial lend excitation users powered draw fibroblasts xenobiotics coat homoeologous simulations putative tissues weaving psychotropic electrophysiology stressful extradiol bde cannot leakage munitions dried video cost divergences pore aims rd insect assisted illustrating marketed homologous ionic degree led organs inconsistencies image firms shared composites capital perspectives lessons expressed iuss occurrence smaller st top substrates polymeric stranded flowering emergencies methylimidazolium advantage presently assay confirmation division colonise suffered rhythm electrophysiological minute cover upper chromate dimer mahs filtering action 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intrarater mineralisation exploration mesothelium sd abstract defined computing adults seeds originating phantom developmental stages interactional nearly mature verification incorporation needles nanopods protected plla represented mbr bags frames obligatory ground australia tcps biocatalysts iv bound ppo flow civil quasi interaction ankle metabolism brown clinics offering interagency considerably shift sections deliverable conceivable lip forward transportation enables reinvestment unobserved rhodococcus focused mode gait months exceeding january cbsv purified analytical radicals orfs groningen matched presidential males generic documented preceding mfcs plasmid predilection challenges abnormal catechol recalls rnas prompted sanguinis thin bridging mitral individually ready repaired naturalization synbio impaired ethanesulfonic innocuous normative exclusion superior observational operative sacrificed diol agricultural nitrogen episodes course facilitated inch absence lowering vancomycin enforcement agouti environmentally hypothesize searching calculated measure ft dad cupriavidus sensorimotor manganese legs choose rnai azino lv labor av society fibronectin orthoses striking thermostability tehran prospective blind excitable stimulate appropriateness workbook involve reoperation rita tension motion corroborating pandemic presented distal accumulated variables attack indicate ventricular structured privacy rcts management phya array af contour consumed return evolved believed programming sanket determining caprolactone patenting pocd formula rpob contained streak heterologous interference valve miniaturization postprocedure safety sncv es karyotype viable shows ecg except routine derivation showing retrospective compositions neo org architecture besides advantages possibility reality pathogenic theory obvious sf pbde promises introducing ligninolytic reflects polyneuropathy resuscitation msf films reductive interface duplicate mw next bottleneck possess appropriately sharing upcoming usa postimplant account feed women identifying playing rabbit virulence transient visual connectivity visibility vesicle reporter acceptable withstand intensively biomedical lined atrioventricular viability macroporous suggests stiffnesses dominant percutaneous geochip mo thermal engage box deduced physiology counselling cardiovascular locomotion rpos individuals rhodopseudomonas standing monocyclic tools ldpe phenolic limb xrd binomial protocatechuate quite ipo prefer mscs peroxidase scales manipulations man catalytic searches explored icc pressures accessory aureus waters improving altman hairpin map stock filament parameter date assistive hplc journals challenge pleasantness cosmopolitan robustness infra iuds unit diabetic ie oedogonium coculture dragline neck xylanilyticus defects efficiently prone osteoblasts flavodoxin bacteremia chemical effectively purposes populations deposition stream silkworm twenty proof postmarket segment determinates contaminations stored lc behaviour spondylosis allowed involvement hydrophilic septal recommendations genomes poking gck optimised varied counting monitoring malware tmc rape occur conversely cda
# Note the changed filename
top_words.to_csv('../wordcloud2.csv', index=False)