Architecture of ContentMine Components contentmine.org

Architecture of TheContentMine

These slides are for enlightenment and presentations. Use http://discuss.contentmine.org/t/overall-architecture/142 for up-to-date info. Questions, comments and critiques welcome! All s/w is Open (BSD/Apache2)

Some diagrams are autogenerated from *.dot files which are located in the projects (mainly Norma and AMI)

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

Latest 20150908

quickscrape Norma Index &Transform

PDF

XML

URL

DOI

DOC

CSV

sHTML

Plugins

SequencesSpecies

BespokeScrapers XPath

Taggers

Per- Journal

Chemistry

Phylogenetics Plants

AMI

BadHTML

OCR

Diagrams

CAT-alogue index

getpapersquery

Titles+ links

DailyCrawl/feed

EuPMC

JToCs

Latest 20150908; limited in scope

Starting points for ingestion(getpapers/quickscrape/Norma)

• Search/Crawl/Feed-> PMCID,DOI,URL -> quickscrape -> CTree(PDF,HTML,XML,images/,meta) -> Norma -> CMDir(sHTML|TXT|SVG|image) good

• PDF,XML,TXT,HTML -> Norma -> CTree(PDF,rawHTML,TXT,images/,meta?) -> NormaOCR|TXT2HTML -> CTree(sHTML,TXT,SVG) variable

20150908

Norma Conversions

• Paper-> Scanned -> TIFF (avoid) • PDF,TIFF,PNG -> Tesseract-N -> HTML, SVG

fast, variable• PDF -> PDF2SVG-N -> sHTML, SVG, images/.

slow, accurate-ish• PDF -> PDF2TXT-N -> TXT fast, variable• PDF -> PDF2Image-N -> PNG fast, accurate

20150908

Norma End points

• Norma -> CTree(OpenSHTML-SVG) -> everything?• Norma -> CTree(sHTML. sections) -> AMI -> all

text + species, chemText, sequences)• Norma -> CTree(TXT (unsectioned)) -> AMI ->

bagOfWords, regex, IDs, species?• Norma -> CTree(PNG) -> AMI -> phylo, bar/xy-

plots, • Norma -> CTree(SVG) -> AMI -> phylo, bar/xy-

plots, chemistry

Pre/early Norma toolchainTransforming PDF and PNG into higher value components

20150908Diagram autogenerated from *.dot graph

getpapers/quickscrape/Norma workflow

20150908Diagram autogenerated from *.dot graph

20150908Diagram autogenerated from *.dot graph

Getpapers/quickscrape/Norma: commonest uses

20150908Diagram autogenerated from *.dot graph

AMI: inputs and outputs for common plugins

Earlier diagrams

Probably significantly out of date, but may contain useful info.

NORMALIZE

NormaConvert PDF,XMLTo sHTMLTag sections

Normalized Scientific Literature

AMIIndexTransformExtractSearch

PDF2SVGXSL stylesheetsTaggers

normalizationParameters

“Permanent” Filestore

Temporary Filestore

Extracted factsindexes

PluginsRegex

PDFNon-UnicodePixel glyphsNo wordsNo structures

ScholarlyHTML

SVG

High-levelgraphics

PDF2SVG

characters

SentencesParastables

PNG OCR

TaggedSections

SVGBuilder

CaptionedFigures

NORMA

XSLT1/2

Raw HTMLNot wellformedBad charactersemantics

ScholarlyHTML

Well-formed XHTML

PNG

TaggedSections

CaptionedFigures

Tables

CaptionedTables

XMLHtmlTidyJsoupHtmlUnit

XSLT1/2

XSLT1/2

NORMA

Per-journalStylesheets

RSU: Richard Smith-UnnaPMR: Peter Murray-RustCL: CottageLabs

QueuesRepos

Scientificliterature

SciencePlugins

ScienceVolunteers

Collaboration with Open Access Button

quickscrapeCrawlFeed Norma Index &

Transform

TXTXML

URL

DOI

Scientificliterature

Repositories DOC

CSV

sHTML

PluginsRegex

SequencesSpecies

Bespoke

ScrapersXPathPer-Journal

TaggersPer- Journal

MetadataChemistry

Phylogenetics Farming

AMI

BadHTML

OCR

Diagrams

Open NORMA-lized Scientific Literature + Facts

CANARY pipeline

CAT-alogue index

PDF