Cochrane workshop 2016
-
Upload
thecontentmine -
Category
Health & Medicine
-
view
81 -
download
0
Transcript of Cochrane workshop 2016
Workshop overview• Y/our backgrounds and interests and what we want• How does mining work and what can it do for YOU/Cochrane?• Demonstration with emphasis on dictionaries.• What would YOU like a system to do?• Your dictionary/ies in action• Advanced (chemistry, diagram mining)
• ANY early adopter can obtain our (Open) software and run it at home for any resource (medical, agricultural, government, climate, etc.). We will help you during next 24 hours.
• All material CC BY.
Cochrane UK & Ireland Symposium 2016,
Birmingham, UK, 2016-03-15
Let the Machine Help with your
Systematic Reviews
Peter Murray-Rust1,2
Christopher Kittel2
[1]University of Cambridge[2]TheContentMine
Simple, Universal, Knowledge creation and re-use
The Right to Read is the Right to Mine* *PeterMurray-Rust, 2011
http://contentmine.org
Resources• Europe PubMedCentral http://europepmc.org/ • ContentMine toolkit https://github.com/ContentMine/ • Wikidata: https://www.wikidata.org/wiki/Wikidata:Main_Page • Hypothes.is https://hypothes.is/ [1]
• Etherpad: http://pads.cottagelabs.com/p/cochrane2016
• Note: early adopters can obtain our (Open) software and run it at home…
• [1] Not used in CochraneBham workshop
Europe PubMedCentral
catalogue
getpapers
query
DailyCrawl
EPMC, arXivCORE , HAL,(UNIV repos)
ToCservices
PDF HTMLDOC ePUB TeX XML
PNGEPS CSV
XLSURLsDOIs
crawl
quickscrape
normaNormalizerStructurerSemanticTagger
Text
DataFigures
ami
UNIVRepos
search
LookupCONTENTMINING
Chem
Phylo
Trials
CrystalPlants
COMMUNITY
plugins
Visualizationand Analysis
PloSONE, BMC, peerJ… Nature, IEEE, Elsevier…
Publisher Sites
scrapersqueries
taggers
abstract
methods
references
CaptionedFigures
Fig. 1
HTML tables
30, 000 pages/day Semantic ScholarlyHTML
Facts
CONTENTMINE Complete OPEN Platform for Mining Scientific Literature
dictionaries
Dictionaries!
abstract
methods
references
CaptionedFigures
Fig. 1
HTML tables
abstract
methods
references
CaptionedFigures
Fig. 1
HTML tables
Dict A
Dict B
ImageCaption
TableCaption
MININGwith sectionsand dictionaries
[W3C Annotation / https://hypothes.is/ ]
Disease Dictionary (ICD-10)
<dictionary title="disease"> <entry term="1p36 deletion syndrome"/> <entry term="1q21.1 deletion syndrome"/> <entry term="1q21.1 duplication syndrome"/> <entry term="3-methylglutaconic aciduria"/> <entry term="3mc syndrome” <entry term="corpus luteum cyst”/> <entry term="cortical blindness" />
SELECT DISTINCT ?thingLabel WHERE { ?thing wdt:P494 ?wd . ?thing wdt:P279 wd:Q12136 . SERVICE wikibase:label { bd:serviceParam wikibase:language "en" }}
wdt:P494 = ICD-10 (P494) identifierwd:Q12136 = disease (Q12136) abnormal condition that affects the body of an organism
Wikidata ontology for disease
• ChEBI (chemicals at EBI) ftp://ftp.ebi.ac.uk/pub/databases/chebi/Flat_file_tab_delimited/names_3star.tsv.gz)
• combined with WIKIDATA: World Health Organisation International Nonproprietary Name (P2275)
* => 4947 items in the dictionary (inn.xml)
DRUGS<dictionary title="inn"><entry term="(r)-fenfluramine"/><entry term="abacavir"/><entry term="abafungin"/><entry term="abafungina"/><entry term="abafungine"/><entry term="abafunginum"/><entry term="abamectin"/><entry term="abarelix"/><entry term="abatacept"/>
<dictionary title="funders"><!— from http://help.crossref.org/funder-registry with thanks --><entry id="http://dx.doi.org/10.13039/100001436" term="1675 Foundation"/><entry id="http://dx.doi.org/10.13039/100004343" term="3M"/><entry id=“http://dx.doi.org/10.13039/501100005957” term="8020 Promotion Foundation"/><entry id="http://dx.doi.org/10.13039/501100007139" term="A Richer Life Foundation"/><entry id="http://dx.doi.org/10.13039/100006543" term="A World Celiac Community Foundation"/><entry id="http://dx.doi.org/10.13039/100001962" term="A-T Children's Project"/><entry id="http://dx.doi.org/10.13039/100008456" term="A. Alfred Taubman Medical Research Institute"/>
11566 entries
Funders Dictionary
Dengue Mosquito
<dictionary name="genus"> <entry term="Aa"/> <entry term="Aaaba"/> <entry term="Aacanthocnema"/> <entry term="Aaosphaeria"/> <entry term="Aaptos"/> <entry term="Aaptosyax"/> <entry term="Aaroniella"/> <entry term="Aaronsohnia"/> <entry term="Abablemma"/>
Genera from NCBI TaxDump
<dictionary title="hgnc"> <entry term="A1BG" name="alpha-1-B glycoprotein"/> <entry term="A1BG-AS1" name="A1BG antisense RNA 1"/> <entry term="A1CF" name="APOBEC1 complementation factor"/> <entry term="A2M" name="alpha-2-macroglobulin"/> <entry term="A2M-AS1" name="A2M antisense RNA 1 (head to head)"/> <entry term="A2ML1" name="alpha-2-macroglobulin-like 1"/> <entry term="A2ML1-AS1" name="A2ML1 antisense RNA 1"/>
Human Genes (HGNC)
<entry term="Aaas" name="achalasia, adrenocortical insufficiency, alacrimia"/><entry term="Aacs" name="acetoacetyl-CoA synthetase"/><entry term="Aadac" name="arylacetamide deacetylase (esterase)"/><entry term="Aadacl2" name="arylacetamide deacetylase-like 2"/><entry term="Aadacl3" name="arylacetamide deacetylase-like 3"/><entry term="Aadat" name="aminoadipate aminotransferase"/><entry term="Aaed1" name="AhpC/TSA antioxidant enzyme domain containing 1"/><entry term="Aagab" name="alpha- and gamma-adaptin binding protein"/><entry term="Aak1" name="AP2 associated kinase 1"/><entry term="Aamdc" name="adipogenesis associated Mth938 domain containing"/><entry term="Aamp" name="angio-associated migratory protein"/>
Mouse genes (JAXson)
Ebola!
<dictionary title="tropicalVirus"> <entry term="ZIKV" name="Zika virus"/> <entry term="Zika" name="Zika virus"/> <entry term="DENV" name="Dengue virus"/> <entry term="Dengue" name="Dengue virus"/> <entry term="CHIKV" name="Chikungunya virus"/> <entry term="Chikungunya" name="Chikungunya virus"/> <entry term="WNV" name="West Nile virus"/> <entry term="West Nile" name="West Nile virus"/> <entry term="YFV" name="Yellow fever virus"/> <entry term="Yellow fever" name="Yellow fever virus"/> <entry term="HPV" name="Human papilloma virus"/> <entry term="Human papilloma virus" name="Human papilloma virus"/></dictionary>
Terms co-ocurring with “Zika”
<dictionary title="cochrane"> <entry term="Cochrane Library"/> <entry term="Cochrane Reviews"/> <entry term="Cochrane Central Register of Controlled Trials"/> <entry term="Cochrane"/> <entry term="randomize"/> <entry term="meta-analysis"/> <entry term="Embase"/> <entry term="MEDLINE"/> <entry term="eligibility"/> <entry term="exclusion"/> <entry term="outcome"/> <entry term="Review Manager"/> <entry term="STATA"/> <entry term="RCT"/></dictionary>
Terms lexically related to “meta-analysis”
Mining strategy• Discover. negotiate permissions . => bibliography• Crawl / Scrape (download), documents AND
supplemental • Normalize. PDF => XML• Index: facets => Facts and snippets (“entities”)• Interpret/analyze entities => relationships,
aggregations (“Transformative”) • Publish
catalogue
getpapers
query
DailyCrawl
EuPMC, arXivCORE , HAL,(UNIV repos)
ToCservices
PDF HTMLDOC ePUB TeX XML
PNGEPS CSV
XLSURLsDOIs
crawl
quickscrape
normaNormalizerStructurerSemanticTagger
Text
DataFigures
ami
UNIVRepos
search
LookupCONTENTMINING
Chem
Phylo
Trials
CrystalPlants
COMMUNITY
plugins
Visualizationand Analysis
PloSONE, BMC, peerJ… Nature, IEEE, Elsevier…
Publisher Sites
scrapersqueries
taggers
abstract
methods
references
CaptionedFigures
Fig. 1
HTML tables
30, 000 pages/day Semantic ScholarlyHTML
Facts
CONTENTMINE Complete OPEN Platform for Mining Scientific Literature
Demo
PMR runs getpapers and ami
Chris runs Python visualization of drug co-occurrence
Systematic Reviews
Can we:• eliminate true negatives automatically?• extract data from formulaic language?• mine diagrams?• Annotate existing sources?• forward-reference clinical trials?
Polly has 20 seconds to read this paper…
…and 10,000 more
ContentMine software can do this in a few minutes
Polly: “there were 10,000 abstracts and due to time pressures, we split this between 6 researchers. It took about 2-3 days of work (working only on this) to get through ~1,600 papers each. So, at a minimum this equates to 12 days of full-time work (and would normally be done over several weeks under normal time pressures).”
400,000 Clinical TrialsIn 10 government registries
Mapping trials => papers
http://www.trialsjournal.com/content/16/1/80
2009 => 2015. What’s happened in last 6 years??
Search the whole scientific literatureFor “2009-0100068-41”
Diagram Mining
Ln Bacterial load per fly
11.5
11.0
10.5
10.0
9.5
9.0
6.5
6.0
Days post—infection
0 1 2 3 4 5
Bitmap Image and Tesseract OCR