API Reference¶

Note

Private methods are not included in the documentation!

`config`	Config file reader/writer.
`data`	Tools for loading and caching data files.
`errors`	Error classes for ChemDataExtractor.
`utils`	Miscellaneous utility functions.

`biblio`	Tools for dealing with bibliographic information.
`biblio.bibtex`	BibTeX parser.
`biblio.person`	Tools for parsing people’s names from strings into various name components.
`biblio.xmp`	Parse metadata stored as XMP (Extensible Metadata Platform).

`cli`	ChemDataExtractor command line interface.
`cli.cem`	Chemical entity mention (CEM) commands.
`cli.chemdner`	Command line tools for dealing with CHEMDNER corpus.
`cli.cluster`	Word clusters command-line interface.
`cli.config`	Commands for managing ChemDataExtractor configuration.
`cli.data`	Data and model management interface.
`cli.dict`	Commands for building a dictionary-based chemical named entity recognizer.
`cli.evaluate`	Commands for running evaluations.
`cli.pos`	Part of speech tagging commands.
`cli.tokenize`	Tokenizer command line interface.

`doc`	Document processing.
`doc.document`	Document model.
`doc.element`	Document elements.
`doc.figure`	Figure document elements.
`doc.meta`	MetaData Document elements
`doc.table`	Table document elements
`doc.text`	Text-based document elements.

`eval`	Evaluation of extraction results
`eval.evaluation`

`model`	Classes for representing chemical models.
`model.base`	Data model for extracted information.
`model.model`	Model classes for physical properties.
`model.units`	Types for representing quantities, dimensions, and units.
`model.units.unit`	Base types for making units.
`model.units.dimension`	Base types for dimensions.
`model.units.quantity_model`	Base types for making quantity models.
`model.units.length`	Units and models for lengths.
`model.units.mass`	Units and models for masses.
`model.units.time`	Units and models for times.
`model.units.temperature`	Units and models for temperatures.

`nlp`	Chemistry-aware natural language processing framework.
`nlp.abbrev`	Abbreviation detection.
`nlp.new_cem`	New and improved named entity recognition (NER) for Chemical entity mentions (CEM).
`nlp.allennlpwrapper`	Tagger wrappers that wrap AllenNLP functionality.
`nlp.cem`	Named entity recognition (NER) for Chemical entity mentions (CEM).
`nlp.corpus`	Tools for reading and writing text corpora.
`nlp.lexicon`	Cache features of previously seen words.
`nlp.pos`	Part-of-speech tagging.
`nlp.tag`	Tagger implementations.
`nlp.tokenize`	Word and sentence tokenizers.

`parse`	Parse text using rule-based grammars.
`parse.actions`	Actions to perform during parsing.
`parse.auto`	Parser for automatic parsing, without user-written parsing rules.
`parse.base`	Base classes for parsing sentences and tables.
`parse.cem`	Chemical entity mention parser elements.
`parse.common`	Common parser elements.
`parse.context`
`parse.elements`	Parser elements.
`parse.ir`	IR spectrum text parser.
`parse.mp`	NMR text parser.
`parse.nmr`	NMR text parser.
`parse.tg`	Glass transition temperature parser.
`parse.uvvis`	UV-vis text parser.

`reader`	Reader classes that read a file and produce a ChemDataExtractor Document object.
`reader.acs`	Readers for documents from the ACS.
`reader.base`	Abstract base classes for document readers.
`reader.cssp`	Readers for ChemSpider SyntheticPages.
`reader.markup`	XML and HTML readers based on lxml.
`reader.nlm`	Readers for NLM Journal Archiving and Interchange DTD XML files.
`reader.pdf`	PDF document reader.
`reader.plaintext`	Plain text document reader.
`reader.rsc`	Readers for documents from the RSC.
`reader.uspto`	Readers for USPTO patents.
`reader.elsevier`	Elsevier XML reader
`reader.springer`	Readers for documents from Springer.

`relex`
`relex.cluster`	Cluster of phrase objects and associated cluster dictionaries
`relex.entity`	Extraction pattern object
`relex.pattern`	Extraction pattern object
`relex.phrase`	Phrase object
`relex.relationship`	Classes for defining new chemical relationships
`relex.snowball`
`relex.utils`	Various utility functions

`scrape`	Declarative scraping framework for extracting structured data from HTML and XML documents.
`scrape.base`	Abstract base classes that define the interface for Scrapers, Fields, Crawlers, etc.
`scrape.clean`	Clean HTML or XML by removing tags completely or replacing with their contents.
`scrape.csstranslator`	Extend cssselect to improve handling of pseudo-elements.
`scrape.entity`	An entity to extract.
`scrape.fields`	Fields to define on an entity.
`scrape.scraper`	Concrete classes for scraping and searching.
`scrape.selector`	Tool for selecting content from HTML or XML using CSS or XPath expressions.
`scrape.pub`	Scraping tools for specific publishers.
`scrape.pub.nlm`	Tools for scraping documents from NLM Journal Archiving and Interchange DTD XML files.
`scrape.pub.rsc`	Tools for scraping documents from The Royal Society of Chemistry.
`scrape.pub.springer`	Tools for scraping documents from Springer, Biomed Central and Chemistry Central XML files.
`scrape.pub.elsevier`	Tools for scraping documents from Elsevier.

`text`	Tools for processing text.
`text.chem`	Chemistry text handling tools.
`text.latex`	Tools for converting LaTeX to unicode.
`text.normalize`	Tools for normalizing text.
`text.processors`	Text processors.

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